Biology subjects

Shahriar, S.

Publications and source records attributed to Shahriar, S..

13 recordsLinked to original sources

bioRxiv2026

Recombinant SIRT1 expression and SIRT1 METTL3 interaction analysis with computational identification of phytochemical SIRT1 activators and inhibitors

Sirtuin 1 (SIRT1), a NAD{+/-}dependent histone deacetylase, regulates diverse biological processes including aging, stress response, and cancer progression. Owing to its dual roles in tumor suppression and promotion, selective modulators of SIRT1 have attracted considerable therapeutic interest. This study explored the interaction of SIRT1 with METTL3 and screened phytochemicals from Indian medicinal plants for potential SIRT1 activation or inhibition. Human SIRT1 (residues 183-665) was cloned, expressed in E. coli, purified, and validated by isothermal titration calorimetry (ITC) to confirm binding with METTL3. Computational approaches, including molecular docking, ADMET profiling, molecular dynamics (MD) simulations, MM-PBSA free energy estimation, and frontier molecular orbital (FMO) analysis, were employed to characterize ligand interactions. Docking revealed Catechin, Epicatechin, Kaempferol, and Bisdemethoxycurcumin as potent inhibitors, showing stronger binding than the reference inhibitor Selisistat by stabilizing the catalytic pocket via key hydrogen bonds and {pi}-{pi} stacking interactions. Among activators, Ginsenosides and Carnosol demonstrated higher affinities than resveratrol, binding the allosteric site through hydrophobic and electrostatic interactions. MD simulations highlighted Catechin and Ginsenosides as the most stable modulators, supported by reduced RMSD, compact Rg values, and favorable hydrogen bond occupancy. MM-PBSA confirmed their strong binding free energies, while ADMET analysis predicted favorable pharmacokinetic properties and low toxicity, particularly for Catechin and Ginsenosides. Overall, this study integrates expression and purification of the protein and computational modeling to identify phytochemicals as potential SIRT1 modulators and provides novel insights into the SIRT1-METTL3 regulatory axis. These findings highlight Catechin and Ginsenosides as promising scaffolds for therapeutic strategies targeting cancer and metabolic disorders.

molecular biology↗

bioRxiv2026

Beyond hazard identification: Discovering mechanisms of action from a ToxCast chemical screen in zebrafish

Large-scale chemical screens are important tools for hazard identification and chemical prioritization, but they less commonly progress from identifying a phenotype to identifying its mechanism. Here, we used zebrafish embryos to screen 4,657 chemicals from the U.S. EPA ToxCast Phase III library for disruption of embryonic development and advanced selected hits through sequential validation using original library stocks, independently sourced chemicals, concentration-response analysis, transcriptomics, and functional experiments. Of 61 primary hits subjected to repeat testing, 33 reproduced the original phenotype, and four of eight compounds subsequently tested using independently sourced chemicals exhibited reproducible concentration-dependent developmental toxicity. We then investigated purpurin, an understudied anthraquinone pigment that caused pericardial edema, circulation defects, and body-axis abnormalities. Transcriptomic analysis of purpurin-exposed embryos revealed coordinated suppression of pathways involved in calcium regulation, ion transport, and neuronal signaling. Increasing extracellular calcium produced a concentration-dependent rescue of purpurin-induced developmental abnormalities, whereas equivalent magnesium supplementation did not, supporting a role for calcium availability or homeostasis in purpurin developmental toxicity. These results demonstrate that large-scale in vivo toxicity screening can be integrated with independent chemical validation and functional follow-up to move beyond hazard identification toward mechanistic understanding of how environmental chemicals disrupt embryonic development.

pharmacology and toxicology↗

bioRxiv2026

Computational Structure Modeling, Functional Characterization, and Identification of Potential Inhibitors for the cyclic-di-GMP Mediated Biofilm Forming Membrane Protein in Vibrio cholerae

Cholera, caused by Vibrio cholerae, continues to pose a serious global public health challenge, with its impact worsened by rising antibiotic resistance associated with bacterial biofilm formation. This study reveals the role of the hypothetical protein (HP) TYC33605.1 in cyclic-di-GMP (c-di-GMP)-mediated biofilm regulation and identifies natural inhibitors that disrupt this mechanism. Functional annotation revealed TYC33605.1 as a membrane-associated diguanylate cyclase (DGC) with GGDEF and sensory domains, critical for c-di-GMP synthesis and biofilm persistence. Homology modelling and molecular dynamics (MD) simulations validated its stable 3D structure (C-score: -1.22, Ramachandran favoured regions: 91.1%) and dynamic behaviour (average RMSD: 8.55 [A]). Virtual molecular docking screening of 1,092 natural compounds identified Luteolin (CID 5280445) and Sativanone (CID 13886678) as top candidates, exhibiting strong binding affinities (-9.1 and -9.0 kcal/mol, respectively) and forming hydrogen bonds, {pi}-cation, and hydrophobic interactions with key residues (Glu293, Arg364, Ala176). MD simulations (100 ns) confirmed complex stability, with Luteolin and Sativanone showing lower RMSD fluctuations (7.78 [A] and 8.13 [A]) compared to the control and apoprotein. The ADME/Tox profiles highlighted favourable pharmacodynamics (PD), pharmacokinetics (PK), high gastrointestinal absorption, no hepatotoxicity, and drug-likeness (Lipinski compliance). Principal component, probability density function, and binding free energy analyses underscore ligand-induced conformational stability. This study proposes the molecular characterisation of the HP and the bioactive compounds Luteolin and Sativanone as promising inhibitors targeting TYC33605.1, offering a novel strategy to combat biofilm-mediated antibiotic resistance and a framework for analogous antimicrobial discovery in Vibrio cholerae.

bioinformatics↗

bioRxiv2026

Brain shuttle target expression levels vary by individual, not by brain region, disease, age, or sex

Therapeutics fused to brain shuttles that exploit endogenous receptor-mediated transport at the blood-brain barrier (BBB) offer a promising strategy to deliver large molecule drugs and biologics to the CNS. A fundamental but untested assumption underlying their clinical development is that their endothelial receptor targets are consistently expressed between individuals and between patient populations. Here, we analyzed gene and protein expression of eleven canonical brain shuttle targets in isolated human brain microvascular endothelial cells and brain microvessels from 11 large cohorts, using single-cell and single-nucleus transcriptomics and quantitative proteomics. Expression was remarkably stable between brain regions, sexes, ages, and normal health versus four major neurodegenerative conditions, Alzheimers disease, Parkinsons disease, Huntingtons disease, and amyotrophic lateral sclerosis, with 612 of 631 comparisons (97%) showing no significant difference. Regional heterogeneity of brain shuttle targets previously reported in rodent models was not observed in human tissue, and disease states had minimal impact in all diseases examined. In striking contrast, target abundance differed consistently among individuals in every demographic and clinical group, for all eleven targets and all data modalities. These findings establish individual receptor abundance as a critical and previously uncharacterized variable for brain shuttle translational research, including clinical trial design and patient stratification.

neuroscience↗

bioRxiv2025

Safe focused ultrasound-mediated blood-brain barrier opening is driven primarily by transient reorganization of tight junctions

Focused ultrasound (FUS) with microbubbles opens the blood-brain barrier (BBB) to allow targeted drug delivery into the brain. The mechanisms by which endothelial cells (ECs) respond to either low acoustic pressures known to open the BBB transiently, or high acoustic pressures that cause brain damage, remain incompletely characterized. Here, we use a mouse strain where tight junctions between ECs are labelled with eGFP and apply FUS at low (450 kPa) and high (750 kPa) acoustic pressures, after which mice are sacrificed at 1 or 72 hours. We find that the EC response leading to FUS-mediated BBB opening at low pressures is localized primarily in arterioles and capillaries, and characterized by a transient loss and reorganization of tight junctions. BBB opening still occurs at low safe pressures in mice lacking caveolae, suggesting that it is driven primarily by transient dismantlement and reorganization of tight junctions. In contrast, BBB opening at high pressures is associated with obliteration of EC tight junctions that remain unrepaired even after 72 hours, allowing continuous fibrinogen passage and persistent microglial activation. Single-cell RNA-sequencing of arteriole, capillary and venule ECs from FUS mice reveals that the transcriptomic responses of ECs exposed to high pressure are dominated by genes belonging to the stress response and cell junction disassembly at both 1 and 72 hours, while lower pressures induce primarily genes responsible for intracellular repair responses in ECs. Our findings suggest that at low pressures transient reorganization of tight junctions and repair responses mediate safe BBB opening for therapeutic delivery. Significance StatementFocused ultrasound with microbubbles is used as a noninvasive method to safely open the BBB at low acoustic pressures for therapeutic delivery into the CNS, but the mechanisms mediating this process remain unclear. Kugelman et al., demonstrate that FUS-mediated BBB opening at low pressures occurs primarily in arterioles and capillaries due to transient reorganization of tight junctions. BBB opening still occurs at low safe pressures in mice lacking caveolae, suggesting a transcellular route-independent mechanism. At high unsafe pressures, cell junctions are obliterated and remain unrepaired even after 72 hours, allowing fibrinogen passage and persistent microglial activation. Single-cell RNA-sequencing supports cell biological findings that safe, FUS-mediated BBB opening may be driven by transient reorganization and repair of EC tight junctions.

bioengineering↗

bioRxiv2024

Control of Molecular Biochemistry and Cell Injury Responses through Highly Ordered Supramolecular Assembly of Flavonoids

Flavonoids are phytonutrients commonly found in plant-based foods and are generally known for their health benefits. However, their utility as potential therapeutics has not been explored because their presence in drug development tests can lead to false positives due to non-specific binding. Here, we employed molecular dynamic simulations (MDS) to examine flavonoid behavior and discovered that they form highly organized supramolecular assemblies that physically interact with disordered regions of enzymatic proteins and can physically interlink multiple protein molecules. These flavonoid assemblies adopt secondary structural patterns like those found in proteins and nucleic acids, and they physically influence molecular movement and tertiary protein structure, thereby modulating the biochemical activities of a diverse range of enzymes. Moreover, in the presence of flavonoids, human cells are protected against injury caused by ultraviolet radiation. These findings unveil a novel form of biochemical regulation wherein small molecules can modulate the function of larger proteins by forming supramolecular assemblies which results in enhanced molecular and cellular resilience. Single Sentence SummaryMolecular dynamic simulations led to the discovery that flavonoid phytonutrients can self-assemble into highly ordered supramolecular structures that interact with enzymatic proteins, slow biochemical activities, and protect cells against injury.

biochemistry↗

bioRxiv2023

A blood-brain-barrier penetrant AAV gene therapy rescues neurological deficits in mucolipidosis IV mice.

Mucolipidosis IV (MLIV) is a rare, autosomal recessive, lysosomal disease characterized by intellectual disability, motor deficits and progressive vision loss. Using AAV9 and AAV-PHP.B as delivery vectors, we previously demonstrated the feasibility of modifying disease course in a mouse model of MLIV by the human MCOLN1 gene transfer. Here, using a primate-enabling capsid AAV.CPP.16 (CPP16), we constructed a new, clinic-oriented MCOLN1 gene expression vector and demonstrated its efficacy in the preclinical model of MLIV. Systemic administration of CPP16-MCOLN1 in adult symptomatic Mcoln1-/- mice at a dose of 1e12 vg per mouse resulted in MCOLN1 expression in the brain and peripheral tissues, alleviated brain pathology, rescued neuromotor function, and completely prevented paralysis. Notable expression of MCOLN1 transcripts was also detected in the retina of the mouse that had exhibited significant degeneration at the time of the treatment. However, no increase of retinal thickness was observed after the gene therapy treatment. Our results suggest a new AAV-based systemic gene replacement therapy for the treatment of MLIV that could be translated into clinical studies.

genetics↗

bioRxiv2023

Rab7a activation promotes degradation of select tight junction proteins at the blood-brain barrier after ischemic stroke

Adherens (AJ) and tight junction (TJ) integrity is critical for blood-brain barrier (BBB) function in the healthy brain. Junction disassembly due to degradation of AJ and TJ proteins leads to acute BBB dysfunction after ischemic stroke, but the mechanisms are not fully understood. Here, we show that endothelial cell deletion of Rab7a, a small GTPase crucial for protein degradation through the endolysosomal system, reduces acute BBB dysfunction and improves neuronal health in mice after ischemic stroke by preventing degradation of select junctional proteins and preserving TJ structural morphology. Two pro-inflammatory cytokines, TNF and IL1{beta}, that trigger barrier disruption in brain endothelial cells (BECs) in vitro and are upregulated in stroke, contribute to Rab7a activation. Silencing Rab7a in vitro partially rescues cytokine-driven barrier disruption in BECs by reducing internalization of some junctional proteins and the formation of F-actin bundles at cell junctions. Rab7a is, therefore, critical for degradation of select junctional proteins during the acute BBB damage after ischemic stroke.

cell biology↗

bioRxiv2023

Glutamatergic neuronal activity regulates angiogenesis and blood-retinal barrier maturation via Norrin/β-catenin signaling

Interactions among neuronal, glial and vascular components are crucial for retinal angiogenesis and blood-retinal barrier (BRB) maturation. Although synaptic dysfunction precedes vascular abnormalities in many retinal pathologies, how neuronal activity, specifically glutamatergic activity, regulates retinal angiogenesis and BRB maturation remains unclear. Using in vivo genetic studies in mice, single-cell RNA-sequencing and functional validation, we show that deep plexus angiogenesis and paracellular BRB maturation are delayed in Vglut1-/- retinas where neurons fail to release glutamate. In contrast, deep plexus angiogenesis and paracellular BRB maturation are accelerated in Gnat1-/- retinas where constitutively depolarized rods release excessive glutamate. Norrin expression and endothelial Norrin/{beta}-catenin signaling are downregulated in Vglut1-/- retinas, and upregulated in Gnat1-/- retinas. Pharmacological activation of endothelial Norrin/{beta}-catenin signaling in Vglut1-/- retinas rescued defects in deep plexus angiogenesis and paracellular BRB maturation. Our findings demonstrate that glutamatergic neuronal activity regulates retinal angiogenesis and BRB maturation by modulating endothelial Norrin/{beta}-catenin signaling.

neuroscience↗

bioRxiv2023

Brain cell type specific proteomics approach to discover pathological mechanisms in the childhood CNS disorder mucolipidosis type IV

1 Mucolipidosis IV (MLIV) is an ultra-rare, recessively inherited lysosomal disorder resulting from inactivating mutations in MCOLN1, the gene encoding the lysosomal cation channel TRPML1. The disease primarily affects the central nervous system (CNS) and manifests in the first year with cognitive and motor developmental delay, followed by a gradual decline in neurological function across the second decade of life, blindness, and premature death in third or fourth decades. Brain pathology manifestations in MLIV are consistent with hypomyelinating leukodystrophy with brain iron accumulation. Presently, there are no approved or investigational therapies for MLIV, and pathogenic mechanisms remain largely unknown. The MLIV mouse model, Mcoln1-/- mice, recapitulates all major manifestations of the human disease. Here, to better understand the pathological mechanisms in the MLIV brain, we performed cell type specific LC-MS/MS proteomics analysis in the MLIV mouse model and reconstituted molecular signatures of the disease in either freshly isolated populations of neurons, astrocytes, oligodendrocytes, and neural stem cells, or whole tissue cortical homogenates from young adult symptomatic Mcoln1-/- mice. Our analysis confirmed on the molecular level major histopathological hallmarks of MLIV universally present in Mcoln1-/- tissue and brain cells, such as hypomyelination, lysosomal dysregulation, and impaired metabolism of lipids and polysaccharides. Importantly, pathway analysis in brain cells revealed mitochondria-related alterations in all Mcoln1-/- brain cells, except oligodendrocytes, that was not possible to resolve in whole tissue. We also report unique proteome signatures and dysregulated pathways for each brain cell population used in this study. These data shed new light on cell-intrinsic mechanisms of MLIV and provide new insights for biomarker discovery and validation to advance translational studies for this disease.

neuroscience↗

bioRxiv2022

Single-cell RNA sequencing implicates venous endothelial cells as a source of VEGF-mediated neo-angiogenesis in neuroinflammation

Histopathological studies of multiple sclerosis (MS), a demyelinating disease of the central nervous system (CNS), and its animal model, experimental autoimmune encephalomyelitis (EAE), have found newly formed leaky vessels in demyelinated acute and chronic plaques, in addition to blood-brain barrier (BBB) damage in existing vessels, that exacerbate disease pathology by increasing infiltration of immune cells. Which vessel subtypes and signaling pathways generate these aberrant vessels is poorly understood. Using single-cell RNA-sequencing and in vivo validation, we find that transcriptome signatures of neo-angiogenesis arise in venous endothelial cells in both acute and chronic EAE, and correlate with upregulation in VEGF-A signaling. These neo-angiogenic markers are also increased in acute and chronic MS lesions. Treatment with a VEGF-A blocking antibody diminishes neo-angiogenic transcriptomic signatures and vascular proliferation in vivo, but does not restore BBB function or ameliorate significantly EAE pathology. Therefore, anti-angiogenic therapies in combination with immunomodulatory therapies may benefit MS progression.

neuroscience↗

bioRxiv2022

Mural norrin/β-catenin signaling regulates Lama2 expression to promote neurovascular unit assembly

Neurovascular unit (NVU) assembly and barrier maturation rely on vascular basement membrane (vBM) composition. Laminins, a major vBM component, are critical for these processes, yet which signaling pathway(s) regulate their expression remains unknown. Here we show that mural cells have active Norrin/{beta}-catenin signaling during central nervous system development. Bulk RNA sequencing and validation using P10 and P14 wild-type versus Apcdd1-/- retinas reveal that Lama2 (Laminin-2 chain) mRNA and protein levels are increased in mutant vasculature undergoing higher Norrin/{beta}-catenin signaling. Mural cells are the main source of Lama2, and {beta}-catenin activation induces Lama2 expression in mural cells in vitro. Markers of mature astrocytes including Aquaporin-4 (a water channel in astrocyte endfeet) and Integrin-6 (a laminin receptor) are upregulated in Apcdd1-/- retinas following higher Lama2 vBM deposition. Thus, the Norrin/{beta}-catenin pathway regulates Lama2 expression in mural cells to promote NVU assembly and neurovascular barrier maturation. SUMMARYBiswas et al., demonstrate that Norrin/{beta}-catenin signaling is active in CNS mural cells and regulates Lama2 deposition in the vascular basement membrane, promoting neurovascular unit assembly and blood-CNS barrier maturation.

developmental biology↗

bioRxiv2020

Effect of sanitation improvements on soil-transmitted helminth eggs in courtyard soil from rural Bangladesh: Evidence from a cluster-randomized controlled trial

Improved sanitation has been hypothesized to reduce soil-transmitted helminth (STH) infections by reducing the prevalence and abundance of STH eggs/larvae in soil. We evaluated the effect of a randomized sanitation program (providing households with an improved dual-pit latrine, tools for child/animal feces management, and behavioral messaging) on reducing STH eggs in soil from household courtyards. We collected soil samples from 1405 households enrolled in the sanitation intervention (n=419) and control (n=914) groups of a cluster-randomized controlled trial (WASH Benefits) in rural Bangladesh approximately 2 years after the initiation of the interventions. We analyzed samples for Ascaris lumbricoides, Trichuris trichiura, and hookworm eggs by microscopy. We estimated prevalence ratios (PR) and relative egg count reductions (ECR) to compare the prevalence of any STH eggs and arithmetic and geometric mean egg counts for any STH per gram of soil between the sanitation and control arms. Among intervention households, latrines achieved high and sustained user uptake by adults while child open defecation remained common and most households did not dispose of child feces hygienically. In courtyard soil from control households, the prevalence of any STH eggs was 75.7% and the prevalence of any larvated STH eggs was 67.3%. A. lumbricoides was detected in 63.0% of control samples and T. trichiura in 55.7% of control samples; hookworm was not detected in any sample. The arithmetic mean egg count for any STH was 3.96 eggs/dry gram, while the geometric mean was 1.58 eggs/dry gram. There was no difference between the intervention and control groups in the prevalence of any STH eggs (PR=0.98 (95% CI: 0.91-1.05)) or mean egg counts (ECR=0.08 (95% CI: -0.10, 0.26) for geometric mean and 0.07 (95% CI: -0.22, 0.37) for arithmetic mean). Adjusted models gave similar results. A compound-level sanitation intervention that provided improved latrines and tools for disposal of child and animal feces did not have an impact on environmental reservoirs of STH eggs. In order to effectively reduce the prevalence and abundance of STH eggs in the environment, sustained, widespread use of sanitation strategies to isolate and hygienically dispose of child and animal feces may need to complement traditional strategies for containment of adult human feces. Author summaryImproved sanitation has been hypothesized to reduce soil-transmitted helminth (STH) infections by reducing the prevalence and abundance of STH eggs/larvae in soil. We evaluated the effect of a randomized sanitation program (providing households with an improved dual-pit latrine, tools for child/animal feces management, and behavioral messaging) on reducing STH eggs in soil from household courtyards. We collected soil samples from 1405 households enrolled in the control and sanitation groups of a cluster-randomized controlled trial (WASH Benefits) in rural Bangladesh approximately 2 years after the initiation of the interventions. We analyzed samples for Ascaris lumbricoides, Trichuris trichiura and hookworm eggs by microscopy. We found no effect of the sanitation intervention on STH eggs in soil. In order to effectively reduce the prevalence and abundance of STH eggs in the environment, sustained, widespread use of sanitation strategies to isolate and hygienically dispose of child and animal feces may need to complement traditional strategies for containment of adult human feces.

ecology↗