Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

Cyclodextrins: Establishing building blocks for AI-driven drug design by determining affinity constants in silico

Cyclodextrins (CDs) are cyclic carbohydrate polymers that hold significant promise for drug delivery and industrial applications. Their effectiveness depends on their ability to encapsulate target molecules with strong affinity and specificity, but quantifying affinities in these systems accurately is challenging for a variety of reasons. Computational methods represent an exceptional complement to in vitro assays because they can be employed for existing and hypothetical molecules, providing high resolution structures in addition to a mechanistic, dynamic, kinetic, and thermodynamic characterization. Here, we employ potential of mean force (PMF) calculations obtained from guided metadynamics simulations to characterize the 1:1 inclusion complexes between four different modified βCDs, with different type, number, and location of substitutions, and two sterol molecules (cholesterol and 7-ketocholesterol). Our methods, validated for reproducibility through four independent repeated simulations per system and different post processing techniques, offer new insights into the formation and stability of CD-sterol inclusion complexes. A systematic distinct orientation preference where the sterol tail projects from the CD's larger face and significant impacts of CD substitutions on binding are observed. Notably, sampling only the CD cavity's wide face during simulations yielded comparable binding energies to full-cavity sampling, but in less time and with reduced statistical uncertainty, suggesting a more efficient approach. Bridging computational methods with complex molecular interactions, our research enables predictive CD designs for diverse applications. Moreover, the high reproducibility, sensitivity, and cost-effectiveness of the studied methods pave the way for extensive studies of massive CD-ligand combinations, enabling AI algorithm training and automated molecular design.

Synthesis and Inclusion Properties of a β-Cyclodextrin Heptaphosphoramidate

In this study, we report a novel per-6-substituted β-cyclodextrin (4) featuring seven phosphoramidate moieties as an innovative host for inclusion. This structurally well-defined host has remarkable water solubility and was isolated in pure form. Analytical techniques such as NMR and ITC were used to probe the molecular interactions with different drug molecules. Our investigations revealed that host 4 can form 2:1 inclusion complexes with various drugs. Further studies showed that the inclusions of drugs by β-CD host (4) are mostly enthalpy driven, highlighting the potential roles played by the phosphoramidate functionalities of the host. Comparatively, a per-O2, O3-acetylated analog (6) of compound 4 was also obtained, which also shows unusual water solubility but diminished inclusion capability.

Enhanced Tumor Targeting and Antitumor Activity of Methylated β-Cyclodextrin-Threaded Polyrotaxanes by Conjugating Cyclic RGD Peptides

We previously reported that acid-degradable methylated β-cyclodextrins (Me-β-CDs)-threaded polyrotaxanes (Me-PRXs) can induce autophagic cell death through endoplasmic reticulum (ER) stress-related autophagy, even in apoptosis-resistant cells. Hence, Me-PRXs show great potential as anticancer therapeutics. In this study, peptide-supermolecule conjugates were designed to achieve the targeted delivery of Me-PRX to malignant tumors. Arg-Gly-Asp peptides are well-known binding motifs of integrin αvβ3, which is overexpressed on angiogenic sites and many malignant tumors. The tumor-targeted cyclic Arg-Gly-Asp (cRGD) peptide was orthogonally post-modified to Me-PRX via click chemistry. Surface plasmon resonance (SPR) results indicated that cRGD-Me-PRX strongly binds to integrin αvβ3, whereas non-targeted cyclic Arg-Ala-Glu (cRGE) peptide conjugated to Me-PRX (cRGE-Me-PRX) failed to interact with integrins αvβ3. In vitro, cRGD-Me-PRX demonstrated enhanced cellular internalization and antitumor activity in 4T1 cells than that of unmodified Me-PRX and non-targeted cRGE-Me-PRX, due to its ability to recognize integrin αvβ3. Furthermore, cRGD-Me-PRX accumulated effectively in tumors, leading to antitumor effects, and exhibited excellent biocompatibility and safety in vivo. Therefore, cRGD conjugation to enhance selectivity for integrin αvβ3-positive cancer cells is a promising design strategy for Me-PRXs in antitumor therapy.

A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors

Class A G protein-coupled receptors (GPCRs), a superfamily of cell membrane signaling receptors, moonlight as constitutively active phospholipid scramblases. The plasma membrane of metazoan cells is replete with GPCRs yet has a strong resting trans-bilayer phospholipid asymmetry, with the signaling lipid phosphatidylserine confined to the cytoplasmic leaflet. To account for the persistence of this lipid asymmetry in the presence of GPCR scramblases, we hypothesized that GPCR-mediated lipid scrambling is regulated by cholesterol, a major constituent of the plasma membrane. We now present a technique whereby synthetic vesicles reconstituted with GPCRs can be supplemented with cholesterol to a level similar to that of the plasma membrane and show that the scramblase activity of two prototypical GPCRs, opsin and the β1-adrenergic receptor, is impaired upon cholesterol loading. Our data suggest that cholesterol acts as a switch, inhibiting scrambling above a receptor-specific threshold concentration to disable GPCR scramblases at the plasma membrane.

A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors

Class A G protein-coupled receptors (GPCRs), a superfamily of cell membrane signaling receptors, moonlight as constitutively active phospholipid scramblases. The plasma membrane of metazoan cells is replete with GPCRs, yet has a strong resting trans-bilayer phospholipid asymmetry, with the signaling lipid phosphatidylserine confined to the cytoplasmic leaflet. To account for the persistence of this lipid asymmetry in the presence of GPCR scramblases, we hypothesized that GPCR-mediated lipid scrambling is regulated by cholesterol, a major constituent of the plasma membrane. We now present a technique whereby synthetic vesicles reconstituted with GPCRs can be supplemented with cholesterol to a level similar to that of the plasma membrane and show that the scramblase activity of two prototypical GPCRs, opsin and the β1-adrenergic receptor, is impaired upon cholesterol loading. Our data suggest that cholesterol acts as a switch, inhibiting scrambling above a receptor-specific threshold concentration to disable GPCR scramblases at the plasma membrane.

Addressing the complexities in measuring cyclodextrin-sterol binding constants: A multidimensional study

A class of cyclodextrin (CD) dimers has emerged as a potential new treatment for atherosclerosis; they work by forming strong, soluble inclusion complexes with oxysterols, allowing the body to reduce and heal arterial plaques. However, characterizing the interactions between CD dimers and oxysterols presents formidable challenges due to low sterol solubility, the synthesis of modified CDs resulting in varying number and position of molecular substitutions, and the diversity of interaction mechanisms. To address these challenges and illuminate the nuances of CD-sterol interactions, we have used multiple orthogonal approaches for a comprehensive characterization. Results obtained from three independent techniques - metadynamics simulations, competitive isothermal titration calorimetry, and circular dichroism - to quantify CD-sterol binding are presented. The objective of this study is to obtain the binding constants and gain insights into the intricate nature of the system, while accounting for the advantages and limitations of each method. Notably, our findings demonstrate ∼1000× stronger affinity of the CD dimer for 7-ketocholesterol in comparison to cholesterol for the 1:1 complex in direct binding assays. These methodologies and findings not only enhance our understanding of CD dimer-sterol interactions, but could also be generally applicable to prediction and quantification of other challenging host-guest complex systems.

Highly sensitive cholesterol concentration trace detection based on a microfiber optic-biosensor enhanced specificity with beta-cyclodextrin film

A beta-cyclodextrin (β-CD) based optic-fiber microfiber biosensor for the detection of cholesterol concentration is propose and experimentally demonstrated. As an identifying substance, β-CD is immobilized on the fiber surface for cholesterol reaction to form an inclusion complex. When the surface refractive index (RI) change is cause because of capturing the complex cholesterol (CHOL), the proposed sensor translates RI change into a macroscopic wavelength drift in the interference spectrum. The microfiber interferometer has a high RI sensitivity of 1251 nm/RIU and a low-temperature sensitivity of -0.019 nm/°C. This sensor can rapidly detect cholesterol in the concentration range of 0.001 to 1 mM and has a sensitivity of 12.7 nm/(mM) in the low concentration range of 0.001 to 0.05 mM. Finally, the characterization by infrared spectroscopy shows that the sensor can indeed detect cholesterol. This biosensor has a few strong advantages of high sensitivity and good selectivity, which expects great potential in biomedical applications.

Self-Assembled Plasmonic Nanojunctions Mediated by Host-Guest Interaction for Ultrasensitive Dual-Mode Detection of Cholesterol

Herein, a fluorescence and surface-enhanced Raman spectroscopy dual-mode system was designed for cholesterol detection based on self-assembled plasmonic nanojunctions mediated by the competition of rhodamine 6G (R6G) and cholesterol with β-cyclodextrin modified on gold nanoparticles (HS-β-CD@Au). The fluorescence of R6G was quenched by HS-β-CD@Au due to the fluorescence resonance energy transfer effect. When cholesterol was introduced as the competitive guest, R6G in the cavities of HS-β-CD@Au was displaced to recover its fluorescence. Moreover, two of HS-β-CD@Au can be linked by one cholesterol to form a more stable 2:1 complex, and then, plasmonic nanojunctions were generated, which resulted in the increasing SERS signal of R6G. In addition, fluorescence and SERS intensity of R6G increased linearly with the increase in the cholesterol concentrations with the limits of detection of 95 and 74 nM, respectively. Furthermore, the dual-mode strategy can realize the reliable and sensitive detection of cholesterol in the serum with good accuracy, and two sets of data can mutually validate each other, which demonstrated great application prospects in the surveillance of diseases related with cholesterol.

Structural Studies of Piperine Inclusion Complexes in Native and Derivative β-Cyclodextrins

Piperine (PN), the primary pungent alkaloid in black pepper shows several biological activities such as antioxidant, antimicrobial and anti-cancerogenic effects. Similar to other alkaloids, PN is characterized by poor water solubility. One way to improve its solubility and thus its biological activities is by forming inclusion complexes with suitable cyclodextrins. In this work PN inclusion complexes in native β-cyclodextrin (β-CD), its methylated (randomly methylated (RM-β-CD), heptakis-(2,6-di-O-methyl)-β-CD (DM-β-CD) and heptakis-(2,3,6-tri-O-methyl)-β-CD (TM-β-CD)) and 2-hydroxypropylated (HP-β-CD) derivatives are investigated using physicochemical methods, such as phase solubility study and X-ray crystallography complemented by theoretical (molecular dynamics simulations) studies. The determination of the crystal structure of the PN inclusion complexes in β-CD, DM-β-CD and TM-β-CD, reveals the formation of 1:2 guest:host inclusion complexes in the crystalline state. The guest PN molecule threads the hydrophobic cavities of the hosts which are arranged as couples in a tail-to-tail mode in the case of PN/β-CD and in a head-to-tail mode in the cases of PN/DM-β-CD and PN/TM-β-CD. MD studies based on the crystallographically determined structures and docked models show the stability of the examined complexes in an aqueous environment whereas the binding affinity of PN for the host molecules is calculated by the MM/GBSA method. Finally, phase-solubility studies of PN with β-CD, RM-β-CD and HP-β-CD are presented, indicating a B_s-type for the PN/β-CD complex and an A_L-type for the PN/RM-β-CD and PN/HP-β-CD complexes with 1:1 guest:host stoichiometry.

Enzyme-Free Liposome Active Motion via Asymmetrical Lipid Efflux

As a class of biocompatible, water-dispersed colloids, liposomes have found widespread applications ranging from food to drug delivery. Adding mobility to these colloids, i.e., liposome micromotors, represents an attractive approach to next-generation liposome carriers with enhanced functionality and effectiveness. Currently, it remains unclear as to the scope of material features useful for building liposome micromotors or how they may differ functionally from their inorganic/polymer counterparts. In this work, we demonstrate liposome active motion taking advantage of mainly a pair of intrinsic material properties associated with these assemblies: lipid phase separation and extraction. We show that global phase separation of ternary lipid systems (such as DPPC/DOPC/cholesterol) within individual liposomes yields stable Janus particles with two distinctive liquid domains. While these anisotropic liposomes undergo pure Brownian diffusion in water, similar to their homogeneous analogues, adding extracting agents, cyclodextrins, to the system triggers asymmetrical cholesterol efflux about the liposomes, setting the latter into active motion. We present detailed analyses of liposome movement and cholesterol extraction kinetics to establish their correlation. We explore various experimental parameters as well as mechanistic details to account for such motion. Our results highlight the rich possibility to hierarchically design lipid-based artificial motors, from individual lipids, to their organization, surface chemistry, and interfacial mechanics.

The influence of unconventional ultrasonic pasteurization on the characteristics of curds obtained from goat milk with the low cholesterol content

This study aimed to evaluate the influence of different power-time ultrasound regimes of pasteurization on the physical, chemical, organoleptic properties, and lipid quality indices of goat curds characterized by a low cholesterol level. Cholesterol was eliminated by a percentage of 92.1 % by treating the raw goat milk with beta-cyclodextrin in the proportion of 0.6 %. Afterward, the goat milk was subjected to the following ultrasound regimes: 320 W for 1 (PA1), 3 (PA3), and 6 min (PA6) and 881 W for 1 (PP1), 3 (PP3), and 6 min (PP6) and then used for the curds production. Due to the ultrasound treatment, the milk suffered a concentration phenomenon, the most accentuated being registered for the PP6 sample. Considering the sensory properties, the most appreciated curd was the one obtained by the PP6 regime which recorded the highest scores for color and taste. Regarding the microbiological aspects, the ability of ultrasounds to inactivate microorganisms is observed and the most accentuated phenomenon is reported in the PP6 case. Thus, in comparison with the control sample, the total number of germs is reduced by a proportion of 91.85 %, the β-glucuronidase-positive Escherichia coli decreased by 93.15 %, while the coagulase-positive staphylococci were completely inactivated for the PP6 curd. The curds obtained for the PA6 and PP6 regimes registered the highest dry matter values as a cause of an accentuated syneresis process. The acidity values were higher for the curds obtained for PA1, PA3, and PA6 regimens due to more pronounced lactose hydrolysis and lower in the cases of PP3 and PP6 regimens compared to the control cheese. Twenty-five saturated, monounsaturated, and polyunsaturated fatty acids were identified in the curd samples and a rise in the unsaturated fatty acids proportion as the intensity of the applied ultrasound regime increased was observed. Also, AI, TI, and H/H lipid quality indices recorded better values as the power and time of the ultrasound action increased.

Platycodin D, a natural component of Platycodon grandiflorum, prevents both lysosome- and TMPRSS2-driven SARS-CoV-2 infection by hindering membrane fusion

An ongoing pandemic of coronavirus disease 2019 (COVID-19) is now the greatest threat to global public health. Herbal medicines and their derived natural products have drawn much attention in the treatment of COVID-19, but the detailed mechanisms by which natural products inhibit SARS-CoV-2 have not been elucidated. Here, we show that platycodin D (PD), a triterpenoid saponin abundant in Platycodon grandiflorum (PG), a dietary and medicinal herb commonly used in East Asia, effectively blocks the two main SARS-CoV-2 infection routes via lysosome- and transmembrane protease serine 2 (TMPRSS2)-driven entry. Mechanistically, PD prevents host entry of SARS-CoV-2 by redistributing membrane cholesterol to prevent membrane fusion, which can be reinstated by treatment with a PD-encapsulating agent. Furthermore, the inhibitory effects of PD are recapitulated by the pharmacological inhibition or gene silencing of NPC1, which is mutated in patients with Niemann-Pick type C (NPC) displaying disrupted membrane cholesterol distribution. Finally, readily available local foods or herbal medicines containing PG root show similar inhibitory effects against SARS-CoV-2 infection. Our study proposes that PD is a potent natural product for preventing or treating COVID-19 and that briefly disrupting the distribution of membrane cholesterol is a potential novel therapeutic strategy for SARS-CoV-2 infection.

Platycodin D, a natural component of Platycodon grandiflorum, prevents both lysosome- and TMPRSS2-driven SARS-CoV-2 infection by hindering membrane fusion

An ongoing pandemic of coronavirus disease 2019 (COVID-19) is now the greatest threat to global public health. Herbal medicines and their derived natural products have drawn much attention in the treatment of COVID-19, but the detailed mechanisms by which natural products inhibit SARS-CoV-2 have not been elucidated. Here, we show that platycodin D (PD), a triterpenoid saponin abundant in Platycodon grandiflorum (PG), a dietary and medicinal herb commonly used in East Asia, effectively blocks the two main SARS-CoV-2 infection routes via lysosome- and transmembrane protease serine 2 (TMPRSS2)-driven entry. Mechanistically, PD prevents host entry of SARS-CoV-2 by redistributing membrane cholesterol to prevent membrane fusion, which can be reinstated by treatment with a PD-encapsulating agent. Furthermore, the inhibitory effects of PD are recapitulated by the pharmacological inhibition or gene silencing of NPC1, which is mutated in patients with Niemann-Pick type C (NPC) displaying disrupted membrane cholesterol distribution. Finally, readily available local foods or herbal medicines containing PG root show similar inhibitory effects against SARS-CoV-2 infection. Our study proposes that PD is a potent natural product for preventing or treating COVID-19 and that briefly disrupting the distribution of membrane cholesterol is a potential novel therapeutic strategy for SARS-CoV-2 infection.

Caffeine-Cyclodextrin Complexes as Solids: Synthesis, Biological and Physicochemical Characterization

Mechanochemical and in-solution synthesis of caffeine complexes with α-, β-, and γ-cyclodextrins was optimized. It was found that short-duration, low-energy cogrinding, and evaporation (instead of freeze-drying) are effective methods for the formation and isolation of these complexes. The products obtained, their pure components, and their mixtures were examined by powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), FT-IR and Raman spectroscopy. Moreover, molecular modeling provided an improved understanding of the association process between the guest and host molecules in these complexes. The complexes were found to exhibit high toxicity in zebrafish (Danio rerio) embryos, in contrast to pure caffeine and cyclodextrins at the same molar concentrations. HPLC measurements of the caffeine levels in zebrafish embryos showed that the observed cytotoxicity is not caused by an increased caffeine concentration in the body of the organism, as the concentrations are similar regardless of the administered caffeine form. Therefore, the observed high toxicity could be the result of the synergistic effect of caffeine and cyclodextrins.

Cyclodextrin dimers: A versatile approach to optimizing encapsulation and their application to therapeutic extraction of toxic oxysterols

We have developed a novel class of specifically engineered, dimerized cyclodextrin (CD) nanostructures for the encapsulation of toxic biomolecules such as 7-ketocholesterol (7KC). 7KC accumulates over time and causes dysfunction in many cell types, linking it to several age-related diseases including atherosclerosis and age-related macular degeneration (AMD). Presently, treatments for these diseases are invasive, expensive, and show limited benefits. CDs are cyclic glucose oligomers utilized to capture small, hydrophobic molecules. Here, a combination of in silico, in vitro, and ex vivo methods is used to implement a synergistic rational drug design strategy for developing CDs to remove atherogenic 7KC from cells and tissues. Mechanisms by which CDs encapsulate sterols are discussed, and we conclude that covalently linked head-to-head dimers of βCDs have substantially improved affinity for 7KC compared to monomers. We find that inclusion complexes can be stabilized or destabilized in ways that allow the design of CD dimers with increased 7KC selectivity while maintaining an excellent safety profile. These CD dimers are being developed as therapeutics to treat atherosclerosis and other debilitating diseases of aging.

Synthesis and Characterization of Cholesteryl Conjugated Lysozyme (CHLysozyme)

Hydrophobic interaction is important for protein conformation. Conjugation of a hydrophobic group can introduce intermolecular hydrophobic contacts that can be contained within the molecule. It is possible that a strongly folded state can be formed in solution compared with the native state. In this study, we synthesized cholesteryl conjugated lysozyme (CHLysozyme) using lysozyme and cholesterol as the model protein and hydrophobic group, respectively. Cholesteryl conjugation to lysozyme was confirmed by nuclear-magnetic resonance. Differential-scanning calorimetry suggested that CHLysozyme was folded in solution. CHLysozyme secondary structure was similar to lysozyme, although circular dichroism spectra indicated differences to the tertiary structure. Fluorescence measurements revealed a significant increase in the hydrophobic surface of CHLysozyme compared with that of lysozyme; CHLysozyme self-associated by hydrophobic interaction of the conjugated cholesterol but the hydrophobic surface of CHLysozyme decreased with time. The results suggested that hydrophobic interaction changed from intramolecular interaction to an intermolecular interaction. Furthermore, the relative activity of CHLysozyme to lysozyme increased with time. Therefore, CHLysozyme likely forms a folded state with an extended durability of activity. Moreover, lysozyme was denatured in 100% DMSO but the local environment of tryptophan in CHLysozyme was similar to that of a native lysozyme. Thus, this study suggests that protein solution stability and resistance to organic solvents may be improved by conjugation of a hydrophobic group.

Cardiac apoptosis caused by elevated cholesterol level in experimental autoimmune myocarditis

It has been reported that cholesterol-lowing agents can ameliorate severity of myocarditis. However, the beneficial effect of the agents has been claimed to be independent of cholesterol reduction as there is no significant change in the plasma cholesterol level in myocarditis. In the present study, using experimental autoimmune myocarditis (EAM) rats as an animal model, we demonstrated that EAM induced elevation of cholesterol level and impaired cholesterol efflux capacity in the cardiac tissue. Moreover, serum high-density lipoprotein (HDL) content was reduced and HDL function associated protein Paraoxonase 1 (PON1) activity was decreased. Besides, the major structural protein within HDL, Apolipoprotein A1 (ApoA1) expression in the cardiac tissues was significantly reduced while the level of serum ApoA1 was not significantly altered. Importantly, cholesterol depleting agent methyl-β-cyclodextrin (MβCD) alleviated the development of EAM, as monitored by decreased ratio of heart weight to body weight (HW/BW), decreased infiltration of inflammatory cells and collagen deposition, improved cardiac function, reduced expression of apoptosis-related protein Bax, Fas, FasL and caspase-3 and increased level of anti-apoptotic protein Bcl-2. These results suggest that reduction of cholesterol level in cardiac tissue could suppress EAM-induced cardiac apoptosis through both intrinsic and extrinsic apoptotic pathways.

Hybrid Plasmonic Fiber-Optic Sensors

With the increasing demand of achieving comprehensive perception in every aspect of life, optical fibers have shown great potential in various applications due to their highly-sensitive, highly-integrated, flexible and real-time sensing capabilities. Among various sensing mechanisms, plasmonics based fiber-optic sensors provide remarkable sensitivity benefiting from their outstanding plasmon-matter interaction. Therefore, surface plasmon resonance (SPR) and localized SPR (LSPR)-based hybrid fiber-optic sensors have captured intensive research attention. Conventionally, SPR- or LSPR-based hybrid fiber-optic sensors rely on the resonant electron oscillations of thin metallic films or metallic nanoparticles functionalized on fiber surfaces. Coupled with the new advances in functional nanomaterials as well as fiber structure design and fabrication in recent years, new solutions continue to emerge to further improve the fiber-optic plasmonic sensors' performances in terms of sensitivity, specificity and biocompatibility. For instance, 2D materials like graphene can enhance the surface plasmon intensity at the metallic film surface due to the plasmon-matter interaction. Two-dimensional (2D) morphology of transition metal oxides can be doped with abundant free electrons to facilitate intrinsic plasmonics in visible or near-infrared frequencies, realizing exceptional field confinement and high sensitivity detection of analyte molecules. Gold nanoparticles capped with macrocyclic supramolecules show excellent selectivity to target biomolecules and ultralow limits of detection. Moreover, specially designed microstructured optical fibers are able to achieve high birefringence that can suppress the output inaccuracy induced by polarization crosstalk and meanwhile deliver promising sensitivity. This review aims to reveal and explore the frontiers of such hybrid plasmonic fiber-optic platforms in various sensing applications.

Molecular structure study of a heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin complex of cholesterol

Heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (2) and cholesterol form a water-soluble complex 3. We performed several NMR studies, particularly ¹H, ¹³C, 2D NOESY and DOSY, at various temperatures on 500 and 950 MHz instruments. We discovered that the complex 3 is unstable above 57 °C in heavy water, while it is kinetically stable enough to be studied by NMR in detail at 1 °C. We demonstrated the formation of a face-to-face 2:1 complex with a binding constant of approximately 2.2 × 10⁶ M^-2.