Diffusion of small molecule drugs is affected by surface interactions and crowder proteins

Underestimated role of macromolecular crowding in bioengineered in vitro models of health and diseases

Macromolecular crowding (MMC) is a ubiquitous phenomenon in biological systems that is largely overlooked in bioengineered in vitro cellular models. This comprehensive review examines the significant impact of both intracellular and extracellular MMC on cellular and molecular processes under physiological and pathological conditions. By synthesizing current knowledge and identifying critical gaps in our understanding of MMC, this review highlights the need to incorporate crowding into the development of in vitro models for studying health and diseases, as well as for drug discovery platforms. The pervasive nature of MMC in biological systems underscores its potential importance in various physiological and pathological processes, including protein aggregation disorders, cancer, and vascular diseases. Recognizing the ubiquitous influence of MMC could open new avenues for therapeutic interventions and deepen our understanding of fundamental biological processes.

Potential Antidiabetic Activity of Nordihydroguaiaretic Acid: An Insight into Its Inhibitory Mechanisms on Carbohydrate-Hydrolyzing Enzymes, the Binding Behaviors with Enzymes, and In Vivo Antihyperglycemic Effect

The inhibitory mechanisms and binding behaviors of nordihydroguaiaretic acid (NDGA) to α-glucosidase/α-amylase were investigated by in vitro multispectroscopic methods and in silico modeling technique. The results demonstrated that NDGA reversibly and uncompetitively inhibited α-glucosidase, exhibiting stronger inhibition than acarbose, while it displayed noncompetitive inhibition against α-amylase. Additionally, NDGA could spontaneously bind to α-glucosidase/α-amylase mainly through hydrogen bonds and hydrophobic forces, thus altering the spatial structure of enzymes and reducing their catalytic activity. The presence of crowding reagents/polysaccharides/undigested milk proteins would decrease the inhibitory ability of NDGA, whereas fatty acids exhibited the opposite phenomenon on α-glucosidase. Furthermore, the antidiabetic activity of NDGA in vivo was evaluated using the diabetic Drosophila model induced by a high-sugar diet. It was found that NDGA significantly reduced the glucose levels of diabetic Drosophila. These findings suggested that NDGA was a potential inhibitor of α-glucosidase/α-amylase and could be used as a nutritional adjuvant to prevent diabetes.

PEG-mCherry interactions beyond classical macromolecular crowding

The dense cellular environment influences bio-macromolecular structure, dynamics, interactions, and function. Despite advancements in understanding protein-crowder interactions, predicting their precise effects on protein structure and function remains challenging. Here, we elucidate the effects of PEG-induced crowding on the fluorescent protein mCherry using molecular dynamics simulations and fluorescence-based experiments. We identify and characterize specific PEG-induced structural and dynamical changes in mCherry. Importantly, we find interactions in which PEG molecules wrap around specific surface-exposed residues in a binding mode previously observed in protein crystal structures. Fluorescence correlation spectroscopy experiments capture PEG-induced changes, including aggregation, suggesting a potential role for the specific PEG-mCherry interactions identified in simulations. Additionally, mCherry fluorescence lifetimes are influenced by PEG and not by the bulkier crowder dextran or by another linear polymer, polyvinyl alcohol, highlighting the importance of crowder-protein soft interactions. This work augments our understanding of macromolecular crowding effects on protein structure and dynamics.

Utility of Brownian dynamics simulations in chemistry and biology: A comprehensive review

Brownian dynamics (BD) simulations, a powerful computer simulation tool that has gained significant attraction in investigating the intricate dynamics of chemical and biological systems. By meticulously modeling the diffusive motion of molecules and their intricate interactions, BD simulations offer invaluable insights into a diverse array of phenomena, including reaction kinetics, molecular transport, and biomolecular association. This comprehensive review delves into the utility of BD simulations within the realms of chemistry and biology. We meticulously explore the theoretical underpinnings of the technique, critically analyze its strengths and limitations, and showcase its diverse applications across various scientific domains. By providing a comprehensive analysis of the existing literature, we aim to illuminate the potential of BD simulations to significantly advance our understanding of complex chemical and biological systems, ultimately contributing to the development of innovative therapeutic solutions serving a broad range of biomedical applications.

Ultrasound-triggered drug release and cytotoxicity of microbubbles with diverse drug attributes

Ultrasound (US)-triggered cavitation of drug-loaded microbubbles (MBs) represents a promising approach for targeted drug delivery, with substantial benefits attainable through precise control over drug release dosage and form. This study investigates Camptothecin-loaded MBs (CPT-MBs) and Doxorubicin-loaded MBs (DOX-MBs), focusing on how properties such as hydrophilicity, hydrophobicity, and charged functional groups affect their interaction with the lipid surfaces of MBs, thereby influencing the fundamental characteristics and acoustic properties of the drug-loaded MBs. In comparison to DOX-MBs, CPT-MBs showed larger MB size (2.2 ± 0.3 and 1.4 ± 0.1 μm, respectively), a 2-fold increase in drug loading, and an 18 % reduction in leakage after 2 h at 37℃. Under 1 MHz US with a 100 ms pulse repetition interval (PRI), 1000 cycles, 5-minute duration, and 550 kPa acoustic pressure, CPT-MBs undergo inertial cavitation, while DOX-MBs undergo stable cavitation. Drug particles released from these MBs under US-induced cavitation were analyzed using dynamic light scattering, NanoSight, cryo-electron microscopy, and density gradient ultracentrifugation. Results showed that CPT-MBs mainly release free CPT, while DOX-MBs release multilayered DOX-lipid aggregates. The cytotoxicity to C6 cells induced by US-triggered cavitation of these two types of MBs also differed. DOX-lipid aggregates delayed initial uptake, leading to less pronounced short-term (2 h) effects compared to the rapid release of free CPT from CPT-MBs. These findings underscore the need to optimize drug delivery strategies by fine-tuning MB composition and US parameters to control drug release kinetics and achieve the best tumoricidal outcomes.

Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells

Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion rates of proteins, their intrinsic structural stability, binding of proteins to their corresponding partners as well as biomolecular organization and phase separation. While such intracellular crowding can have a large impact on biomolecular structure and function, the molecular mechanisms and driving forces that determine the effect of crowding on dynamics and conformations of macromolecules are so far not well understood. At a molecular level, computational methods can provide a unique lens to investigate the effect of macromolecular crowding on biomolecular behavior, providing us with a resolution that is challenging to reach with experimental techniques alone. In this review, we focus on the various physics-based and data-driven computational methods developed in the past few years to investigate macromolecular crowding and intracellular protein condensation. We review recent progress in modeling and simulation of biomolecular systems of varying sizes, ranging from single protein molecules to the entire cellular cytoplasm. We further discuss the effects of macromolecular crowding on different phenomena, such as diffusion, protein-ligand binding, and mechanical and viscoelastic properties, such as surface tension of condensates. Finally, we discuss some of the outstanding challenges that we anticipate the community addressing in the next few years in order to investigate biological phenomena in model cellular environments by reproducing in vivo conditions as accurately as possible.

Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration

For drugs to be active they have to reach their targets. Within cells this requires crossing the cell membrane, and then free diffusion, distribution, and availability. Here, we explored the in-cell diffusion rates and distribution of a series of small molecular fluorescent drugs, in comparison to proteins, by microscopy and fluorescence recovery after photobleaching (FRAP). While all proteins diffused freely, we found a strong correlation between pKa and the intracellular diffusion and distribution of small molecule drugs. Weakly basic, small-molecule drugs displayed lower fractional recovery after photobleaching and 10- to-20-fold slower diffusion rates in cells than in aqueous solutions. As, more than half of pharmaceutical drugs are weakly basic, they, are protonated in the cell cytoplasm. Protonation, facilitates the formation of membrane impermeable ionic form of the weak base small molecules. This results in ion trapping, further reducing diffusion rates of weakly basic small molecule drugs under macromolecular crowding conditions where other nonspecific interactions become more relevant and dominant. Our imaging studies showed that acidic organelles, particularly the lysosome, captured these molecules. Surprisingly, blocking lysosomal import only slightly increased diffusion rates and fractional recovery. Conversely, blocking protonation by N-acetylated analogues, greatly enhanced their diffusion and fractional recovery after FRAP. Based on these results, N-acetylation of small molecule drugs may improve the intracellular availability and distribution of weakly basic, small molecule drugs within cells.

Antioxidant Activity and Hypoallergenicity of Egg Protein Matrices Containing Polyphenols from Citrus Waste

This study reports on the interactions of egg proteins, which represent a major health concern in food allergy, with polyphenols obtained from orange and lemon peels. The antioxidant properties of such citrus peel extracts prior to protein binding were evaluated. The resulting edible, and therefore inherently safe, matrices exhibit reduced IgE binding compared to pure proteins in indirect immunological assays (ELISA) using individual sera from patients allergic to ovalbumin and lysozyme. The reduced allergenicity could arise from the interactions with polyphenols, which alter the structure and functionality of the native proteins. It is hypothesized that the anti-inflammatory and antioxidant properties of the polyphenols, described as inhibitors of the allergic response, could add immunomodulatory features to the hypoallergenic complexes. A docking analysis using lysozyme was conducted to scrutinize the nature of the protein-polyphenol interactions. An in silico study unravelled the complexity of binding modes depending on the isoforms considered. Altogether, the presented results validate the antioxidant properties and reduced allergenicity of polyphenol-fortified proteins. Lastly, this study highlights the upgrading of vegetable wastes as a source of natural antioxidants, thus showing the benefits of a circular economy in agri-food science.

Fluorescence photobleaching and recovery of fluorescein sodium in carbomer film

This study investigated fluorescence photobleaching and the recovery of fluorescein sodium (FS)-loaded carbomer films. To mitigate errors caused by the self-quenching effect, the experiments were conducted at FS concentrations of 0.1, 0.5, and 1 wt%. The results revealed a nonlinear relationship between fluorescence intensity and FS concentration (0.1-1 wt%). Moreover, the degree and rate of photobleaching increased with FS concentration. The recovery level and recovery rate exhibited contrasting relationships with FS concentration. Higher FS concentrations were associated with a longer recovery time, which can be attributed to the prolonged irradiation, resulting in a bleached region that was larger than the initially irradiated area.

Fluorescent liposomal nanocarriers for targeted drug delivery in ischemic stroke therapy

Ischemic stroke causes acute CNS injury and long-term disability, with limited treatment options such as surgical clot removal or clot-busting drugs. Neuroprotective therapies are needed to protect vulnerable brain regions. The purinergic receptor P2X4 is activated during stroke and exacerbates post-stroke damage. The chemical compound 5-(3-Bromophenyl)-1,3-dihydro-2H-Benzofuro[3,2-e]-1,4-diazepin-2-one (5BDBD) inhibits P2X4 and has shown neuroprotective effects in rodents. However, it is difficult to formulate for systemic delivery to the CNS. The current manuscript reports for the first time, the synthesis and characterization of 5BDBD PEGylated liposomal formulations and evaluates their feasibility to treat stroke in a preclinical mice model. A PEGylated liposomal formulation of 5BDBD was synthesized and characterized, with encapsulation efficacy of >80%, and release over 48 hours. In vitro and in vivo experiments with Nile red encapsulation showed cytocompatibility and CNS infiltration of nanocarriers. Administered 4 or 28 hours after stroke onset, the nanoformulation provided significant neuroprotection, reducing infarct volume by ∼50% compared to controls. It outperformed orally-administered 5BDBD with a lower dose and shorter treatment duration, suggesting precise delivery by nanoformulation improves outcomes. The fluorescent nanoformulations may serve as a platform for delivering and tracking therapeutic agents for stroke treatment.

What's past is prologue: FRAP keeps delivering 50 years later

Fluorescence recovery after photobleaching (FRAP) has emerged as one of the most widely utilized techniques to quantify binding and diffusion kinetics of biomolecules in biophysics. Since its inception in the mid-1970s, FRAP has been used to address an enormous array of questions including the characteristic features of lipid rafts, how cells regulate the viscosity of their cytoplasm, and the dynamics of biomolecules inside condensates formed by liquid-liquid phase separation. In this perspective, I briefly summarize the history of the field and discuss why FRAP has proven to be so incredibly versatile and popular. Next, I provide an overview of the extensive body of knowledge that has emerged on best practices for quantitative FRAP data analysis, followed by some recent examples of biological lessons learned using this powerful approach. Finally, I touch on new directions and opportunities for biophysicists to contribute to the continued development of this still-relevant research tool.