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Gabr, M.

Publications and source records attributed to Gabr, M..

69 records · Page 4Linked to original sources

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↗

HTS-Oracle: A Retrainable AI Platform for High-Confidence Hit Identification Across Difficult-to-Drug Targets

Despite rapid advances in computational drug discovery, high-throughput screening (HTS) remains the primary method for identifying initial hits, particularly for targets with limited tractability to small molecules. Yet conventional HTS campaigns are costly and inefficient, often yielding hit rates below 2% and discarding valuable negative data. Here we present HTS-Oracle, a retrainable, deep learning-based platform that integrates transformer-derived molecular embeddings (ChemBERTa) with classical cheminformatics features in a multi-modal ensemble framework for hit prediction. We applied HTS-Oracle to the immune co-stimulatory receptor CD28, a prototypical difficult-to-drug target, and prioritized 345 candidates from a chemically diverse library of 1,120 small molecules. Experimental screening via temperature-related intensity change (TRIC) identified 29 hits (8.4% hit rate), representing an eightfold improvement over conventional methods such as surface plasmon resonance (SPR), TRIC, and affinity selection mass spectrometry (ASMS)-based HTS. By enriching true positives and filtering out non-binders upfront, HTS-Oracle streamlines the discovery pipeline and enables more focused, cost-effective screening. Two hit compounds disrupted the CD28-B7.1 interaction, with orthogonal validation provided by MST, ELISA, and molecular dynamics simulations. HTS-Oracle reduces screening burden and improves discovery efficiency, offering a powerful, scalable, and experimentally validated AI framework for accelerating hit identification across difficult-to-drug targets.

bioinformatics↗

Small Molecule-Based Blockade of CD28 Suppresses T Cell Costimulation Across Cellular and Mucosal Co-culture Models

Background and PurposeCD28 is a pivotal costimulatory receptor that governs T cell activation through interaction with B7 ligands (CD80/CD86). While antibody-based inhibitors of CD28 signaling have advanced clinically, the development of small molecule modulators remains limited due to the receptors shallow, flexible surface. We sought to discover small-molecule modulators with favorable pharmacokinetic properties capable of disrupting CD28-B7 interactions in translational models of T cell activation. Experimental ApproachStructure-based virtual screening was conducted using pharmacophore filtering and consensus docking against the human CD28 ectodomain. Hit compounds were validated using temperature-related intensity change (TRIC) and microscale thermophoresis (MST). Functional antagonism was assessed through ELISA, NanoBit luciferase complementation, and a CD28 Blockade Bioassay. In vitro ADME and safety pharmacology profiling were performed, and immunosuppressive activity was evaluated in tumor-PBMC and mucosal-PBMC co-culture assays. Key ResultsLead compound 22VS bound CD28 in biophysical screening, targeting a lipophilic canyon anchored by K24, Q25, and P27. 22VS inhibited CD28-CD80/CD86 interactions in ELISA and cell-based assays with submicromolar potency. 22VS robustly suppressed T cell activation markers in both tumor- PBMC and human mucosal epithelial-PBMC co-culture models, phenocopying the anti-CD28 biologic FR104. It showed no cytotoxicity up to 300 {micro}M and exhibited high solubility, low clearance, strong membrane permeability, and minimal off-target effects in pharmacokinetic screens. Conclusion and ImplicationsThis study identifies a novel druggable site on CD28 and validates 22VS as a selective, non-toxic small molecule inhibitor with translational potential for immune modulation in autoimmunity, transplantation, and cancer. Bullet Point SummaryO_ST_ABSWhat is already knownC_ST_ABSO_LICD28 is a key T cell costimulatory receptor essential for immune activation. C_LIO_LISmall-molecule inhibitors of CD28 are largely unexplored compared to biologics. C_LI What this study addsO_LIIdentifies a novel druggable pocket on CD28 via structure-based virtual screening. C_LIO_LIDiscovers 22VS, a selective small molecule CD28 inhibitor with cellular activity. C_LIO_LIDemonstrates that 22VS suppresses T cell activation in tumor-PBMC and mucosal-PBMC co- culture assays, phenocopying a benchmark biologic (FR104). C_LIO_LIEstablishes 22VS as a drug-like compound with favorable in vitro pharmacokinetic properties, including metabolic stability, permeability, and low off-target toxicity. C_LI Clinical significanceO_LIHighlights the potential of 22VS as a lead for immunomodulatory therapeutic development. C_LIO_LISupports small-molecule targeting of CD28-B7 interactions in T cell-driven diseases. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/665260v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@f1d2forg.highwire.dtl.DTLVardef@451c98org.highwire.dtl.DTLVardef@158446corg.highwire.dtl.DTLVardef@1f42ef1_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

TRIC Coupled with TR-FRET as a High-Throughput Screening Platform for the Discovery of SLIT2 Binders: A Proof-of-Concept Approach

SLIT2, a secreted glycoprotein involved in axon guidance, immune modulation, and tumor progression, remains largely unexplored as a pharmacological target due to the absence of small-molecule modulators. Here, we present a proof-of-concept high-throughput screening platform that integrates Temperature-Related Intensity Change (TRIC) technology with time-resolved Forster resonance energy transfer (TR-FRET) to identify small molecules capable of disrupting the SLIT2/ROBO1 interaction. Screening a lipid metabolism-focused compound library (653 molecules) yielded bexarotene, as the most potent small molecule SLIT2 binder reported to date, with a dissociation constant (KD) of 2.62 {micro}M. Follow-up TR-FRET assays demonstrated dose-dependent inhibition of SLIT2/ROBO1 interaction, with an IC50 value of [~]22.8 {micro}M and maximal inhibition of [~]15- 25%. These findings suggest a novel extracellular activity of bexarotene and validate the combined use of TRIC and TR-FRET as a scalable screening strategy for SLIT2-targeted small molecules. This platform lays the groundwork for future high-throughput discovery efforts against SLIT2 and its signaling axis. Graphical abstractTRIC-based small molecule screening platform protocol steps with implementation of TR-FRET for the identification of SLIT2 inhibitors. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/663693v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@e585fborg.highwire.dtl.DTLVardef@bf3de5org.highwire.dtl.DTLVardef@178910dorg.highwire.dtl.DTLVardef@7b2086_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Discovery of an Achiral Small Molecule TREM2 Agonist with Im-proved Pharmacokinetic Profile and Validated Target Engagement

The triggering receptor expressed on myeloid cells 2 (TREM2) is a lipid-sensing immunoreceptor on microglia that has emerged as a therapeutic target for Alzheimers disease. Here, we report the discovery of C1, an achiral structural analog of VG-3927--the first small molecule TREM2 agonist to enter clinical development. C1 was synthesized via a modular and enantioselective-free route using sequential Suzuki couplings, enabling rapid scaffold diversification. Compared to VG-3927, the stereochemically simplified derivative (C1) exhibits superior microglial phagocytosis and validated target engagement. C1 induces TREM2 activation in HEK293-hTREM2/DAP12 cells, and its direct binding to TREM2 was confirmed using both microscale thermophoresis (MST) and surface plasmon resonance (SPR). Importantly, C1 also demonstrates a superior pharmacokinetic profile to VG-3927, including enhanced metabolic stability in human and mouse microsomes, favorable PAMPA permeability, and a LogD7.4 compatible with CNS penetration. Docking studies suggested a potential binding mode of C1 at the extracellular domain of TREM2, revealing key polar and hydrophobic interactions. These findings position C1 as a synthetically accessible and pharmacokinetically favorable lead for the development of TREM2-targeted therapies

pharmacology and toxicology↗

Discovery of a First-in-Class SLIT2 Binder Disrupting the SLIT2/ROBO1 Axis via DNA-Encoded Library (DEL) Screening

The SLIT2/ROBO1 signaling axis plays a critical role in neural development, immune regulation, and tumor progression, including glioblastoma. However, small molecule inhibitors targeting this protein-protein interaction remain unexplored. Herein, we report the discovery and validation of DEL-S1, a first-in-class small molecule that binds to SLIT2 and disrupts its interaction with ROBO1. Using a DNA-encoded library (DEL) screen of 4.2 billion compounds, DEL-S1 was identified and confirmed to bind SLIT2 via temperature-related intensity change (TRIC) assay. Functional inhibition of the SLIT2/ROBO1 complex by DEL-S1 was demonstrated using a Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) assay, yielding an IC50 of 68.8 {+/-} 12.5 {micro}M. Molecular docking and molecular dynamics (MD) simulations revealed key interaction hotspots at the SLIT2 binding interface and confirmed that DEL-S1 impairs SLIT2/ROBO1 complex formation by inducing conformational rearrangements. DEL-S1 exhibited favorable ADME properties, including satisfactory plasma and microsomal stability, low cytotoxicity, and minimal hERG liability. To facilitate structure-activity relationship (SAR) exploration, we designed and implemented a modular, one-pot synthetic route leveraging cyanuric chloride reactivity, enabling rapid derivatization of the triazine scaffold of DEL-S1. This strategy yielded structurally diverse analogs, including water-soluble carboxylate derivatives with preserved SLIT2/ROBO1 inhibitory activity. Together, this work establishes a novel chemical scaffold targeting SLIT2 and introduces a flexible synthetic platform to support further optimization toward therapeutic development.

biochemistry↗

Surface Plasmon Resonance (SPR)-Based Workflow for High-Throughput Discovery of CD28-Targeted Small Molecules

CD28 is a critical costimulatory receptor involved in T cell activation and immune regulation, making it a compelling target for immunomodulatory therapies. Despite its therapeutic relevance, small molecule CD28 inhibitors remain largely underexplored. To address this gap, we developed a high-throughput screening (HTS) workflow using surface plasmon resonance (SPR) to identify novel CD28-targeted small molecules. To our knowledge, this work represents the first SPR-based HTS platform applied to the discovery of small molecules targeting a stimulatory immune checkpoint receptor. A chemical library composed of diverse 1,056 small molecules was screened using a 384-well format. Compounds were evaluated based on level of occupancy (LO), binding response, and dissociation kinetics, resulting in 12 primary hits (1.14% hit rate). Follow-up dose-response SPR screening confirmed micromolar-range affinities for three compounds. Molecular docking and 100 ns molecular dynamics (MD) simulations of the top hit, DDS5, revealed a stable complex with CD28, maintained by hydrogen bonding and a persistent interaction with Phe93. Functional validation using a competitive ELISA confirmed that DDS5 inhibited the CD28-CD80 interaction. These results demonstrate that our SPR-based HTS platform is a robust and efficient strategy for discovering CD28-targeted small molecules. The integration of computational evaluation and orthogonal validation further underscores the potential of DDS5 as an early-stage immunomodulatory agent.

pharmacology and toxicology↗

TREM2 Hit Discovery Using TRIC Technology: A Proof-of-Concept High-Throughput Screening Approach

Triggering receptor expressed on myeloid cells 2 (TREM2) is an immunomodulatory receptor implicated in both neurodegenerative diseases and cancer. Depending on the context, TREM2 agonists or inhibitors hold therapeutic potential. To date, the majority of TREM2-targeted strategies have centered on monoclonal antibodies (mAbs), which face limitations such as poor tissue penetration and potential immunogenic side effects. To overcome these challenges and expand the chemical space for TREM2-targeting agents, we developed a high-throughput screening (HTS) platform to identify novel small molecule TREM2 binders. Using temperature-related intensity change (TRIC) technology in a 384-well plate format (NanoTemper Dianthus), we screened two focused compound libraries comprising over 1,200 molecules. From this screen, 18 preliminary hits (1.44% hit rate) were identified and subsequently validated by dose-response binding studies using microscale thermophoresis (MST), yielding four validated hits (0.32% hit rate) with binding affinities in the high to medium micromolar range (e.g., T2337, KD = 22.4 M). The binding of the top hit, T2337, was further validated using surface plasmon resonance (SPR). Additionally, we assessed the functional activity of all four validated hits in a cellular assay measuring TREM2-mediated Syk phosphorylation in HEK293 cells co-expressing human TREM2 and its adaptor protein DAP12. These findings establish a robust and scalable platform for the discovery of small molecule TREM2 modulators and serve as a proof-of-concept for broader HTS campaigns targeting TREM2.

pharmacology and toxicology↗

TRIC-Based High-Throughput Screening Enables the Discovery of Small Molecule CD28 Binders

CD28 is a pivotal costimulatory receptor involved in T cell activation and immune regulation, positioning it as a key therapeutic target for inflammatory diseases, including inflammatory bowel disease (IBD). Despite its potential, small molecules targeting CD28 are still limited. To fill this gap, we developed a high-throughput screening (HTS) platform based on Temperature-Related Intensity Change (TRIC) technology, enabling rapid, immobilization-free screening of chemical libraries of small molecules. Using the Dianthus instrument, we applied our optimized TRIC assay for CD28 (signal-to-noise ratio of 21.99) to screen two MedChemExpress libraries: Small Molecule Immuno-Oncology Compounds (SMIOC) and Protein-Protein Interaction Inhibitors (PPII), identifying 50 initial hits. Following exclusion of compounds with dye interference or aggregation artifacts, 12 candidates were prioritized for further validation. Microscale thermophoresis (MST) confirmed dose-dependent binding of seven compounds to CD28, with affinities in the micromolar range. Surface plasmon resonance (SPR) further validated two compounds, EABP 02303 and CTEP, as CD28 binders. These results demonstrate that our TRIC-based HTS platform is robust, scalable, and effective for identifying small molecule CD28 binders. The incorporation of orthogonal validation supports the reliability of our findings and highlights the feasibility of small-molecule discovery targeting CD28.

biophysics↗

TREM2 Activation by First-in-Class Direct Small Molecule Agonists: DEL Screening, Optimization, Biophysical Validation, and Functional Characterization

Triggering receptor expressed on myeloid cells 2 (TREM2) is a key regulator of microglial function, and its loss-of-function variants are linked to Alzheimers disease (AD) and neurodegenerative disorders. While TREM2 activation is a promising therapeutic strategy, no small molecule agonists acting via direct TREM2 binding have been reported to date. Here, we describe the discovery of first-in-class, direct small molecule TREM2 agonists identified through DNA-encoded library (DEL) screening. The DEL hit (4a) demonstrated TREM2 binding affinity, as validated by three biophysical screening platforms (TRIC, MST, and SPR), induced Syk phosphorylation, and enhanced microglial phagocytosis. Preliminary optimization yielded 4i, which maintained TREM2 engagement with improved selectivity over TREM1 and no cytotoxicity. Molecular dynamics simulations revealed that 4a stabilizes a transient binding pocket on TREM2, suggesting a novel mechanism for receptor activation. These findings provide the first proof-of-concept for direct pharmacological TREM2 agonism, offering a foundation for developing therapeutics against AD and related disorders. Table of Contents graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/655617v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@14a3d24org.highwire.dtl.DTLVardef@f423deorg.highwire.dtl.DTLVardef@5ee108org.highwire.dtl.DTLVardef@107e6df_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

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↗

From Virtual Screens to Cellular Target Engagement: New Small Molecule Ligands for the Immune Checkpoint LAG-3

Herein, we performed a virtual screening study to discover new scaffolds for small molecule-based ligands of the immune checkpoint lymphocyte-activation gene 3 (LAG-3). Molecular dynamics (MD) simulations using the LAG-3 structure revealed two putative binding sites for small molecules: the antibody interface and a lipophilic canyon. A 3D pharmacophore screening resulted in the identification of potential ligands for these binding sites and afforded a library of 25 compounds. We then evaluated the screening hits for LAG-3 binding via microscale thermophoresis (MST) and surface plasmon resonance (SPR). Our biophysical screening identified two binders with KD values in the low micromolar range, compounds 3 (antibody interface) and 25 (lipophilic canyon). Furthermore, we investigated the ability of LAG-3 hits to en-gage LAG-3 on a cellular level using a cellular thermal shift assay (CETSA), where compound 3 emerged as a promising candidate for future development.

pharmacology and toxicology↗

Discovery of ICOS-targeted small molecules using affinity selection mass spectrometry screening

Inducible T cell co-stimulator (ICOS) is a positive immune checkpoint receptor expressed on the surface of activated T cells, which could promote cell function after being stimulated with ICOS ligand (ICOS-L). Although clinical benefits have been reported in the ICOS modulation-based treatment for cancer and autoimmune disease, current modulators are restricted in biologics, whereas ICOS-targeted small molecules are lacking. To fill this gap, we performed an affinity selection mass spectrometry (ASMS) screening for ICOS binding using a library of 15,600 molecules. To the best of our knowledge, this is the first study that utilizes ASMS screening to discover small molecules targeting immune checkpoints. Compound 9 with a promising ICOS/ICOS-L inhibitory profile (IC50 = 29.38 {+/-} 3.41 {micro}M) was selected as the template for the modification. Following preliminary structure-activity relationship (SAR) study and molecular dynamic (MD) simulation revealed the critical role of the ortho-hydroxy group on compound 9 in the ICOS binding, as it could stabilize the interaction via the hydrogen bond formation with residuals on the glycan, and the depletion could lead to an activity lost. This work validates a promising inhibitor for the ICOS/ICOS-L interaction, and we anticipate future modifications could provide more potent modulators for this interaction.

pharmacology and toxicology↗

Design and Biophysical Characterization of Second-Generation Cyclic Peptide LAG-3 Inhibitors for Cancer Immunotherapy

Lymphocyte activation gene 3 (LAG-3) is an inhibitory immune checkpoint crucial for suppressing the immune response against cancer. Blocking LAG-3 interactions enables T cells to recover their cytotoxic capabilities and diminishes the immunosuppressive effects of regulatory T cells. A cyclic peptide (Cys-Val-Pro-Met-Thr-Tyr-Arg-Ala-Cys, disulfide bridge: 1-9) was recently reported as a LAG-3 inhibitor. Based on this peptide, we designed 19 derivatives by substituting tyrosine residue to maximize LAG-3 inhibition. Screening via TR-FRET assay identified 8 outperforming derivatives, with cyclic peptides 12 [Tyr6(L-3-CN-Phe)], 13 [Tyr6(L-4-NH2-Phe)], and 17 [Tyr6(L-3,5-DiF-Phe)] as top candidates. Cyclic peptide 12 exhibited the highest inhibition (IC50 = 4.45 {+/-} 1.36 {micro}M). MST analysis showed cyclic peptides 12 and 13 bound LAG-3 with KD values of 2.66 {+/-} 2.06 {micro}M and 1.81 {+/-} 1.42 {micro}M, respectively, surpassing the original peptide (9.94 {+/-} 4.13 {micro}M). Docking simulations indicated enhanced binding for cyclic peptide 12, with a docking score of -7.236 kcal/mol compared to -5.236 kcal/mol for the original peptide.

pharmacology and toxicology↗

The use of autologous skeletal muscle-derived cells as a sling in the treatment of induced stress urinary incontinence, an experimental study

Introduction & hypothesisThis is an experimental pre-clinical study testing for the applicability of autologous skeletal muscle derived cells as a seeded sling for the treatment of SUI in the canine model Methods10 Mongrel dogs: In 4, skeletal muscle biopsy was harvested from Biceps Femoris. 1 month later, incontinence was induced in 8 dogs through surgical disruption of the pubourethral ligaments. Muscle biopsy was incubated in DMEM medium and after expansion for 8 weeks, MDCs were collected. PGA scaffold was immersed in culture medium, coated with matrigel and cells were seeded. The sling was placed suburethrally in 8 dogs; 2 of which were cell-seeded and 4 had the scaffold only. Urethral pressure (UP) measurement was done at baseline and 2 weeks alter insertion of the sling. The urethra with its surrounding was harvested 4 weeks after sling insertion for histopathology. 2 dogs were considered as control, in which no urethrolysis or insertion of slings were carried out ResultsUP show increase of maximum urethral pressure during static measurement in all dogs with a scaffold inserted. The increase ranged from 5-40 cmH20 (Median 23 cmH20) Histopathology shows significant periurethral proliferation of skeletal muscles in 4 dogs with cell-seeded scaffold, as demonstrated by Desmin. This was maximum in dogs # 1& 2. This was not the case in the 4 dogs that had PGA sling only. ConclusionThe use of skeletal muscle -seeded PGA scaffold is a practical technique with preserved integrity of histological differentiation in canine model at short term. Brief SummaryAutologous Skeletal muscle-derived cells could be propagated in vitro and seeded to PGS scaffolds and used as slings

developmental biology↗