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  1. Abstract

    Understanding kinase‐inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A‐1) of the insulin‐like growth factor‐I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine‐arginine‐aspartic acid (HRD) and aspartic acid‐phenylalanine‐glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C‐helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.

     
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    Free, publicly-accessible full text available March 20, 2025
  2. Abstract

    Sepsis, whole‐body inflammation caused by the contamination of blood by bacteria and endotoxins, affects millions of patients annually with high mortality rates. A recent promising approach to treat sepsis involves the removal of bacteria and endotoxins using extracorporeal blood‐cleansing devices. However, poor specificity, slow recognition of pathogens, and high costs remain the main limitations. Here, the melanin, a biologically derived pigment, is reported for the rapid binding of bacteria and endotoxins from the contaminated blood . This novel approach utilizes the specific binding between Zn2+‐loaded melanin and bacteria/endotoxins with minimal nonspecific interactions with human blood components. Melanin contains various chemical functional groups that allow reversible chelation of metallic ions such as Zn2+via redox reactions. Zn2+enables rapid and specific binding with bacteria/endotoxins due to the strong electrostatic interactions between Zn2+and phosphate ions. The presence of various zinc‐binding proteins on the bacterial cell membrane further enhances the binding. The well‐known biocompatibility and low cost make melanin an ideal material to interface with human blood. Zn2+‐charged melanin can remove 90% ofE. coliand 100% of endotoxin in PBS and human blood. Zn2+‐melanin also demonstrated excellent hemocompatibility shown by protein adsorption, blood coagulation, and hemolysis tests.

     
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    Free, publicly-accessible full text available December 28, 2024
  3. Abstract

    Although tissue culture plastic has been widely employed for cell culture, the rigidity of plastic is not physiologic. Softer hydrogels used to culture cells have not been widely adopted in part because coupling chemistries are required to covalently capture extracellular matrix (ECM) proteins and support cell adhesion. To create an in vitro system with tunable stiffnesses that readily adsorbs ECM proteins for cell culture, a novel hydrophobic hydrogel system is presented via chemically converting hydroxyl residues on the dextran backbone to methacrylate groups, thereby transforming non‐protein adhesive, hydrophilic dextran to highly protein adsorbent substrates. Increasing methacrylate functionality increases the hydrophobicity in the resulting hydrogels and enhances ECM protein adsorption without additional chemical reactions. These hydrophobic hydrogels permit facile and tunable modulation of substrate stiffness independent of hydrophobicity or ECM coatings. Using this approach, it is shown that substrate stiffness and ECM adsorption work together to affect cell morphology and proliferation, but the strengths of these effects vary in different cell types. Furthermore, it is revealed that stiffness‐mediated differentiation of dermal fibroblasts into myofibroblasts is modulated by the substrate ECM. The material system demonstrates remarkable simplicity and flexibility to tune ECM coatings and substrate stiffness and study their effects on cell function.

     
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  4. Abstract

    3D continuous mesoscale architectures of nanomaterials possess the potential to revolutionize real‐time electrochemical biosensing through higher active site density and improved accessibility for cell proliferation. Herein, 3D microporous Ti3C2TXMXene biosensors are fabricated to monitor antibiotic release in tissue engineering scaffolds. The Ti3C2TX‐coated 3D electrodes are prepared by conformal MXene deposition on 3D‐printed polymer microlattices. The Ti3C2TXMXene coating facilitates direct electron transfer, leading to the efficient detection of common antibiotics such as gentamicin and vancomycin. The 3D microporous architecture exposes greater electrochemically active MXene surface area, resulting in remarkable sensitivity for detecting gentamicin (10–1 mM) and vancomycin (100–1 mM), 1000 times more sensitive than control electrodes composed of 2D planar films of Ti3C2TXMXene. To characterize the suitability of 3D microporous Ti3C2TXMXene sensors for monitoring drug elution in bone tissue regeneration applications, osteoblast‐like (MG‐63) cells are seeded on the 3D MXene microlattices for 3, 5, and 7 days. Cell proliferation on the 3D microporous MXene is tracked over 7 days, demonstrating its promising biocompatibility and its clinical translation potential. Thus, 3D microporous Ti3C2TXMXene can provide a platform for mediator‐free biosensing, enabling new applications for in vivo monitoring of drug elution.

     
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  5. Abstract

    Three-dimensional (3D) bio-printing is a rapidly growing field attempting to recreate functional tissues for medical and pharmaceutical purposes. The printability of multiple materials encapsulating various living cells can take this emerging effort closer to tissue regeneration. In our earlier research, we designed a Y-like nozzle connector system capable of switching materials between more than one filament with continuous deposition. The device had a fixed switching angle, was made from plastic, and was suitable for one-time use. This paper presents the extension of our previously proposed nozzle system. We considered 30°, 45°, 60°, and 90° angles (vertical and tilted) between the two materials and chose stainless steel as a material to fabricate those nozzle connectors. The overall material switching time was recorded and compared to analyze the effects of those various angles. Our previously developed hybrid hydrogel (4% Alginate and 4% Carboxymethyl Cellulose, CMC) was used as a test material to flow through the nozzle system. These in-house fabricated nozzle connectors are reusable, easy to clean, and sterile, allowing smooth material transition and flow.

     
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    Free, publicly-accessible full text available June 12, 2024
  6. Abstract

    Among various available 3D bioprinting techniques, extrusion-based three-dimensional (3D) bio-printing allows the deposition of cell-laden bio-ink, ensuring predefined scaffold architecture that may offer living tissue regeneration. With a combination of unique characteristics such as biocompatibility, less cell toxicity, and high-water content, natural hydrogels are a great candidate for bio-ink formulation for the extrusion-based 3D bioprinting process. However, due to its low mechanical integrity, hydrogel faces a common challenge in maintaining structural ty. To tackle this challenge, we characterized the rheological properties of a set of hybrid hydrogels composed of cellulose-derived nanofiber (TEMPO-mediated nano-fibrillated cellulose, TONFC), carboxymethyl cellulose (CMC) and commonly used alginate. A total of 46 compositions were prepared using higher (0.5% and 1.0%) and lower percentages (0.005% and 0.01%) of TONFC, 1%–4% of CMC, and 1%–4% of alginate to analyze the rheological properties. The shear thinning coefficients of n and K were determined for each composition from the flow diagram and co-related with the 3D printability. The ability to control rheological properties with various ratios of a nanofiber can help achieve a 3D bio-printed scaffold with defined scaffold architecture.

     
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    Free, publicly-accessible full text available June 12, 2024
  7. Abstract

    Due to its inbuilt ability to release biocompatible materials encapsulating living cells in a predefined location, 3D bioprinting is a promising technique for regenerating patient-specific tissues and organs. Among various 3D bioprinting techniques, extrusion-based 3D bio-printing ensures a higher percentage of cell release, ensuring suitable external and internal scaffold architectures. Scaffold architecture is mainly defined by filament geometry and width. A systematic selection of a set of process parameters, such as nozzle diameter, print speed, print distance, extrusion pressure, and material viscosity, can control the filament geometry and width, eventually confirming the user-defined scaffold porosity. For example, carefully selecting two sets of process parameters can result in a similar filament width. However, the lack of availability of sufficient analytical relations between printing process parameters and filament width creates a barrier to achieving defined scaffold architectures with available resources. In this paper, filament width was determined using an image processing technique and an analytical relationship was developed, including various process parameters to maintain defined filament width variation for different hydrogels within an acceptable range to confirm the overall geometric fidelity of the scaffold. Proposed analytical relations can help achieve defined scaffold architectures with available resources.

     
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    Free, publicly-accessible full text available June 12, 2024
  8. Abstract

    Due to the three-dimensional nature of the 3D bio-printed scaffolds, typical stagnant cell culturing methods don’t ensure entering medium inside areas or passing through the scaffolds. The bioreactor has frequently provided the required growth medium to encapsulated- and seeded-cells in 3D bio-printed scaffolds. To address this issue, we developed a customized perfusion bioreactor to supply the growth medium dynamically to the cells encapsulated or seeded in the scaffolds. The dynamic supply of fresh growth medium may help improve cell viability and proliferation. Because of its uniform nutrition distribution and flow-induced shear stress within the tissue-engineering scaffold, perfusion bioreactors have been used in a variety of tissue engineering applications. Including a modified setup of our designed bioreactor may improve the in vivo stimuli and conditions, eventually enhancing the overall performance of tissue regeneration. In this paper, we explored the response of fluid flow to certain types of scaffold pore geometries and porosities. We used a simulation technique to determine fluid flow turbulence through various pore geometries such as uniform triangular, square, diamond, circular, and honeycomb. We used variable pore sizes of the scaffold maintaining constant porosity to analyze the fluid flow. Based on the results, optimum designs for scaffolds were determined.

     
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    Free, publicly-accessible full text available June 12, 2024
  9. Abstract

    Three-dimensional (3D) bioprinting is a promising technique for creating patient-specific 3D scaffolds of tissues or organs. An appropriate culturing process is critical to confirm encapsulated and seeded cells’ excellent viability and proliferation into scaffolds materials. Traditional stagnant cell culturing methods don’t ensure entering medium inside areas or passing through the scaffolds. To resolve this issue, we developed a customized perfusion bioreactor to supply the growth medium dynamically to the encapsulated or seeded cells. Our custom-designed bioreactor improves the in vivo stimuli and conditions, which may enhance cell viability and proliferation performance. A design of a dual medium tank was utilized allowing the replacement of already-used medium without interrupting perfusion. Accommodating an array of cassettes in a newly designed perfusion chamber allowed a wide range of scaffolds with various size and shapers to hold. In this paper, we explored fluid flow response on scaffolds fabricated with various material compositions with different viscosities. We fabricated scaffolds following a 00–900 deposition pattern with 8% Alginate, 4% Alginate-4% Carboxymethyl Cellulose (CMC), and 2% Alginate-6% CMC incubated, allowing a constant fluid flow for various periods such as 1, 2, 4, and 8 hours. The change of scaffolds fabricated with multiple material compositions was determined in terms of swelling rate, i.e., change of filament width, and material diffusion, i.e., comparison of dry material weight before and after incubation. This comparative study can assist in application-based materials selection suitable for incubating in a perfusion bioreactor.

     
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    Free, publicly-accessible full text available June 12, 2024
  10. Abstract

    Phosphodiesterase‐5 (PDE5) is responsible for regulating the concentration of the second messenger molecule cGMP by hydrolyzing it into 5′‐GMP. PDE5 is implicated in erectile dysfunction and cardiovascular diseases. The substrate binding site in the catalytic domain of PDE5 is surrounded by several dynamic structural motifs (including the α14 helix, M‐loop, and H‐loop) that are known to switch between inactive and active conformational states via currently unresolved structural intermediates. We evaluated the conformational dynamics of these structural motifs in the apo state and upon binding of an allosteric inhibitor (evodiamine) oravanafil, a competitive inhibitor. We employed enhanced sampling‐based replica exchange solute scaling (REST2) method, principal component analysis (PCA), time‐lagged independent component analysis (tICA), molecular dynamics (MD) simulations, and well‐tempered metadynamics simulations to probe the conformational changes in these structural motifs. Our results support a regulatory mechanism for PDE5, where the α14 helix alternates between an inward (lower activity) conformation and an outward (higher activity) conformation that is accompanied by the folding/unfolding of the α8′ and α8″ helices of the H‐loop. When the allosteric inhibitor evodiamine is bound to PDE5, the inward (inactive) state of the α14 helix is preferred, thus preventing substrate access to the catalytic site. In contrast, competitive inhibitors of PDE5 block catalysis by occupying the active site accompanied by stabilization of the outward conformation of the α14 helix. Defining the conformational dynamics underlying regulation of PDE5 activation will be helpful in rational design of next‐generation small molecules modulators of PDE5 activity.

     
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