Biology subjects

Al-Ali, H.

Publications and source records attributed to Al-Ali, H..

8 recordsLinked to original sources

bioRxiv2026

AGC kinase homology requires and enables co-targeting for CNS regeneration

Axon regrowth in the central nervous system (CNS) is constrained by robust regulatory networks. Here we show that optimal neurite outgrowth in rodent and human CNS neurons is achieved by co-inhibition of kinases across four closely related clades within the protein kinase A, G, and C (AGC) family. The kinases derive from ancestral regulators of cytoskeletal dynamics, resource allocation, and polarized cell growth. Their shared domain architecture makes polypharmacology (co-engagement by a single small molecule) feasible. Phenotype-guided optimization of a tool compound with established efficacy in mouse spinal cord injury models yielded TMP-316, a drug candidate engaging these AGC kinases with selectivity against the broader kinome. A single intrathecal dose of TMP-316 produced sustained motor recovery in a rat cervical hemicontusion model. These findings reveal conditions under which polypharmacology is simultaneously required and enabled by shared evolutionary origins, illuminating a therapeutic discovery principle for pathologies governed by functionally overlapping targets.

neuroscience↗

bioRxiv2026

Lumbar intrathecal catheterization in rats targeting the cerebral cortex: a drug delivery method and validation

Intrathecal (IT) drug delivery is a critical technique for bypassing the blood-brain and blood-spinal cord barriers in preclinical CNS research. However, conventional rat catheterization methods suffer from high rates of neurologic complications, poor reliability, and unverified dosing due to epidural reflux and inconsistent supraspinal distribution. Our objective was to develop and validate an improved method for lumbar IT catheterization in rats that ensures distribution to the brain and to confirm supraspinal pharmacodynamic target engagement. We describe a refined microsurgical technique using dural puncture under direct visual control at the L6-S1 interlaminar space, a site chosen for its anatomical safety margin. The method uses a small-bore (0.33 mm OD) polyurethane (PU) catheter to minimize durotomy size, air-bubble tracking to compensate for catheter dead volume, and epidural sealing with Surgifoam(R) to minimize reflux. Visualization using Evans Blue dye confirmed complete neuraxial distribution from a single 30 {micro}L lumbar bolus injection, with dye reaching the ventral/dorsal brain cisterns. Pharmacodynamic validation of cortical exposure was achieved using an S6 kinase 1 (S6K1) inhibitor. Lumbar IT administration over a period of 6 hours via a pump resulted in significant supraspinal S6K1 engagement, demonstrated by a reproducible reduction in S6 phosphorylation in the cerebral cortex. HighlightsO_LIMethod for lumbar intrathecal catheterization in rats under direct visual control, using basic surgical tools C_LIO_LICNS distribution validated by Evans Blue dye reaching ventral and dorsal brain C_LIO_LIPharmacodynamic confirmation of supraspinal target engagement following lumbar intrathecal delivery of a small molecule kinase inhibitor C_LIO_LIServes as a faithful preclinical model for therapeutics intended for clinical intrathecal administration C_LIO_LIProvides a screening route for early-stage compounds not yet optimized for CNS penetrance, supporting efficacy testing prior to medicinal chemistry investment C_LI

neuroscience↗

bioRxiv2026

Development of NanoBRET cellular target engagement assays in primary neurons for activating mutants of p21-activated kinase 1

The p21-activated kinases (PAKs) are a group of serine-threonine kinases central to multiple signaling pathways that govern cell survival and proliferation. Aberrant activity of PAK1, the most well characterized member of the PAK family, drives progression of several malignancies and brain disorders, including Alzheimers disease and neurodevelopmental disorders. Despite growing interest in PAK1 as a drug target for these diseases, there is no assay to evaluate the intracellular target engagement of PAK1 inhibitors. To address this need, we developed first-in-class NanoBRET assays for wild-type PAK1 and a neurodevelopmental disorder-causing gain-of-function PAK1 mutant. Furthermore, we executed our novel PAK1 NanoBRET assay to evaluate target engagement of PAK1 inhibitors in primary hippocampal neurons. To the best of our knowledge, this is the first demonstration of a NanoBRET cellular target engagement assay in primary neurons, thereby increasing the relevance of our work by confirming PAK1 inhibitor binding to the aberrant form of the protein in primary neurons.

pharmacology and toxicology↗

bioRxiv2025

Novel Lipophagy Inducers as Potential Therapeutics for Lipid Metabolism Disorders

Dysregulation of lipid homeostasis is associated with a wide range of pathologies encompassing neurological, metabolic, cardiovascular, oncological, and renal disorders. We previously showed that lipid droplet (LD) accumulation in podocytes contributes to the progression of diabetic kidney disease (DKD) and reducing LDs preserves podocyte function and prevents albuminuria. Here, we sought to identify compounds that treat pathological LD accumulation. We developed a phenotypic assay using human podocytes and deployed it to screen a combinatorial library comprising over 45 million unique small molecules. This led to the identification of a compound series that effectively reduce LD accumulation in stressed podocytes. Mechanistic studies revealed that these compounds activate lipophagy, reduce LD accumulation, and rescue podocytes from cell death. In contrast, compounds known to induce general autophagy failed to mimic these effects, indicating a novel lipophagy-specific mechanism of action (MoA), which was confirmed with unbiased phenotypic profiling. An advantage of this therapeutic strategy is its potential to not only halt the progression of pathological lipid accumulation but also reverse it. These compounds will serve as tools for uncovering novel drug targets and therapeutic MoAs for treating DKD and other diseases with similar etiologies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=39 SRC="FIGDIR/small/642628v1_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@16039e2org.highwire.dtl.DTLVardef@7865c3org.highwire.dtl.DTLVardef@60e886org.highwire.dtl.DTLVardef@41db90_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

The cyclin-G associated kinase (GAK) is a novel mitotic kinase and therapeutic target in diffuse large B-cell lymphoma

New drug targets are needed for diffuse large B-cell lymphoma (DLBCL), the most common lymphoma subtype, to enable enable development better treatments for patients not cured by standard care. We conducted a phenotypic screen of kinase inhibitors and identified the cyclin G-associated kinase (GAK) as a tumor-selective target. Though GAK is previously described primarily as a participant in membrane trafficking, we found its kinase activity is a key mitotic regulator in DLBCL. Inhibition caused G2/M-phase arrest, chromosome misalignment, and spindle distortion, effects absent in non-malignant controls. Transcriptomics data from clinical samples showed increased GAK expression associates with RB1 deficiency in DLBCL cases, suggesting dependency on GAK linked to retinoblastoma associated protein (RB) loss of function, a common DLBCL driver. RB-deficient DLBCL cells treated with a selective GAK tool compound showed complete arrest at G2/M, pronounced distortion of mitotic spindles, and widespread chromosomal damage. High-content live-cell imaging revealed onset of mitotic catastrophe in response to GAK inhibition, which was more rapid and severe in isogenic cells with RB1 deletion. No GAK-selective inhibitors suitable for clinical development are currently available, but several drugs approved or under development inhibit GAK activity even more potently than thier intended clinical targets. For instance, OTS167, developed against MELK for use in solid tumors, has particularly potent anti-GAK potency and has achieved single-agent tumor-burden reduction in vivo against a DLBCL patient-derived xenograft. GAK is therefore a novel mitotic kinase in DLBCL, linked to the common, undruggable RB loss of function biomarker, and suitable for rapid clinical translation through drug repurposing. SignificanceWe identify cyclin-G associated kinase (GAK) as a novel therapeutic vulnerability in diffuse large B-cell lymphoma. Clinical kinase inhibitors with GAK activity create an opportunity for rapid therapeutic translation through drug repurposing.

cancer biology↗

bioRxiv2022

Empagliflozin reduces renal lipotoxicity in experimental Alport syndrome

Sodium-glucose cotransporter-2 inhibitors (SGLT2i) are anti-hyperglycemic agents that prevent glucose reabsorption in proximal tubular cells. SGLT2i improves renal outcomes in both diabetic and non-diabetic patients, indicating it may have beneficial effects beyond glycemic control. Here, we demonstrate that SGLT2i affects energy metabolism and renal lipotoxicity in experimental Alport syndrome (AS). In vitro, we found that SGLT2 protein expression levels in human and mouse podocytes were similar to tubular cells. Newly established immortalized podocytes from Col4a3 knockout mice (AS podocytes) accumulate lipid droplets along with increased apoptosis when compared to wildtype podocytes. Treatment with SGLT2i empagliflozin reduces lipid droplet accumulation and apoptosis in AS podocytes. Empagliflozin inhibits the utilization of glucose/pyruvate as a metabolic substrate in AS podocytes. In vivo, we demonstrate that empagliflozin reduces albuminuria and prolongs the survival of AS mice. Empagliflozin-treated AS mice show decreased serum blood urea nitrogen and creatinine levels in association with reduced triglyceride and cholesterol ester content in kidney cortices when compared to AS mice. Lipid accumulation in kidney cortices correlates with the decline in renal function. In summary, empagliflozin reduces renal lipotoxicity and improves kidney function in experimental AS in association with the energy substrates switch from glucose to fatty acids in podocytes.

cell biology↗

bioRxiv2019

The Kinase Chemogenomic Set (KCGS): An open science resource for kinase vulnerability identification

We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS) is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.

cell biology↗

bioRxiv2017

Progress Towards a Public Chemogenomic Set for Protein Kinases and a Call for Contributions

Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.

pharmacology and toxicology↗