Role of RNA G-Quadruplexes in the Japanese Encephalitis Virus Genome and Their Recognition as Prospective Antiviral Targets

G-quadruplexes (GQs) have been primarily studied in the context of cancer and neurodegenerative pathologies. However, recent research has shifted focus to their existence and functional roles in viral genomes, revealing GQ-regulated key pathways in various human pathogenic viruses. While GQ structures have been reported in the genomes of emerging and re-emerging viruses, RNA viruses have been understudied compared to DNA viruses, including notable examples such as human immunodeficiency virus-1, hepatitis C virus, Ebola virus, Nipah virus, Zika virus, and SARS-CoV-2. The flavivirus family, comprising the Japanese encephalitis virus (JEV), poses a significant global threat due to recurring outbreaks yet lacks approved antivirals. In this study, we identified and characterized eight putative G-quadruplex-forming motifs within essential genes involved in genome replication, assembly, and internalization in the host cell, conserved across different JEV isolates. The formation and stability of these motifs were validated through a multitude of biophysical and cell-based assays. The interaction and binding affinity of these motifs with the known GQ-binding ligand BRACO-19 were supported by biophysical assays, confirming the capability of these motifs to form GQ structures. Notably, BRACO-19 also exerted antiviral properties through reduction of viral replication and infectious virus titers as well as inhibition of viral protein expression, as evaluated by the cell-based assays. This comprehensive molecular characterization of G-quadruplex structures within the JEV genome highlights their potential as promising antiviral targets for intervention strategies against JEV infection through GQ-specific ligands.

Propofol Protects the Blood-Brain Barrier After Traumatic Brain Injury by Stabilizing the Extracellular Matrix via Prrx1: From Neuroglioma to Neurotrauma

The purpose of this study is to explore the shared molecular pathogenesis of traumatic brain injury (TBI) and high-grade glioma and investigate the mechanism of propofol (PF) as a potential protective agent. By analyzing the Chinese glioma genome atlas (CGGA) and The Cancer Genome Atlas (TCGA) databases, we compared the transcriptomic data of high-grade glioma and TBI patients to identify common pathological mechanisms. Through bioinformatics analysis, in vitro experiments and in vivo TBI model, we investigated the regulatory effect of PF on extracellular matrix (ECM)-related genes through Prrx1 under oxidative stress. The impact of PF on BBB integrity under oxidative stress was investigated using a dual-layer BBB model, and we explored the protective effect of PF on tight junction proteins and ECM-related genes in mice after TBI. The study found that high-grade glioma and TBI share ECM instability as an important molecular pathological mechanism. PF stabilizes the ECM and protects the BBB by directly binding to Prrx1 or indirectly regulating Prrx1 through miRNAs. In addition, PF reduces intracellular calcium ions and ROS levels under oxidative stress, thereby preserving BBB integrity. In a TBI mouse model, PF protected BBB integrity through up-regulated tight junction proteins and stabilized the expression of ECM-related genes. Our study reveals the shared molecular pathogenesis between TBI and glioblastoma and demonstrate the potential of PF as a protective agent of BBB. This provides new targets and approaches for the development of novel neurotrauma therapeutic drugs.

Molecular Tailoring Approach for the Direct Estimation of Individual Noncovalent Interaction Energies in Molecular Systems

The noncovalent interactions (NCIs) are omnipresent in chemistry, physics, and biology. The study of such interactions offers insights into various physicochemical phenomena. Some indirect approaches proposed in the literature for exploring the NCIs are briefly reviewed in Section 1 of this Perspective. These include: (i) Shift in the stretching frequency of an X-Y bond involved in X-Y···Z interaction. (ii) Topological analysis of molecular electron density. (iii) Empirical equations derived employing experimental and theoretical quantities. However, a direct method for estimating individual intramolecular/intermolecular interaction energies has been conspicuous by its absence from the literature. We have developed a molecular tailoring approach (MTA)-based method enabling a direct and reliable estimation of the energy of intra- as well as intermolecular interactions. This method offers a direct and reliable estimation of these interactions, in particular of the hydrogen bonds (HB) in molecules/weakly bound clusters along with the respective cooperativity contribution. In Section 2, the basis of our method is discussed, along with some illustrative examples. The application of this method to a variety of molecules and clusters, with a special emphasis on estimating the HB energy along with the energy of other NCIs is presented in Section 3. Section 4 discusses some computational strategies for applying our method to large molecular clusters. The last Section provides a summary and a discussion on future developments.

Tryptophan As a New Member of RNA-Induced Silencing Complexes Prevents Colon Cancer Liver Metastasis

Essential amino acids (EAA) and microRNAs (miRs) control biological activity of a cell. Whether EAA regulates the activity of miR has never been demonstrated. Here, as proof-of-concept, a tryptophan (Trp, an EAA) complex containing Argonaute 2 (Ago2) and miRs including miR-193a (Trp/Ago2/miR-193a) is identified. Trp binds miR-193a-3p and interacts with Ago2. Trp/Ago2/miR-193a increases miR-193a-3p activity via enhancing Argonaute 2 (Ago2) RNase activity. Other miRs including miR-103 and miR-107 in the Trp complex enhance miR-193a activity by targeting the same genes. Mechanistically, the Trp/Ago2/miR-193a complex interacts with Trp-binding pockets of the PIWI domain of Ago2 to enhance Ago2 mediated miR activity. This newly formed Ago2/Trp/miR-193a-3p complex is more efficient than miR-193a-3p alone in inhibiting the expression of targeted genes and inhibiting colon cancer liver metastasis. The findings show that Trp regulates miR activity through communication with the RNA-induced silencing complexes (RISC), which provides the basis for tryptophan based miR therapy.

Sarmentol H derived from Sedum sarmentosum Bunge directly targets FXR to mitigate cholestasis by recruiting SRC-1

BACKGROUND

Farnesoid X receptor (FXR) is a vital receptor for bile acids and plays an important role in the treatment of cholestatic liver disease. In addition to traditional bile acid-based steroidal agonists, synthetic alkaloids are the most commonly reported non-steroidal FXR agonists. Sarmentol H is a nor-sesquiterpenoid obtained from Sedum sarmentosum Bunge, and in vitro screening experiments have shown that it might be related to the regulation of the FXR pathway in a previous study.

PURPOSE

To investigate the therapeutic effects of sarmentol H on cholestasis and to determine whether sarmentol H directly targets FXR to mitigate cholestasis. Furthermore, this study aimed to explore the key amino acid residues involved in the binding of sarmentol H to FXR through site-directed mutagenesis.

METHODS

An intrahepatic cholestasis mouse model was established to investigate the therapeutic effects of sarmentol H on cholestasis. In vitro experiments, including Co-Ip and FXR-EcRE-Luc assays, were performed to assess whether sarmentol H activates FXR by recruiting the receptor coactivator SRC1. CETSA, SIP, DARTS, and ITC were used to determine the binding of sarmentol H to FXR protein. The key amino acid residues for sarmentol H binding to FXR were analyzed by molecular docking and site-directed mutagenesis. Finally, we conducted in vivo experiments on wild-type and Fxr-/- mice to further validate the anticholestatic target of sarmentol H.

RESULTS

Sarmentol H had significant ameliorative effects on the pathological conditions of cholestatic mice induced with ANIT. In vitro experiments suggested that it is capable of activating FXR and regulating downstream signaling pathways by recruiting SRC1. The target validation experiments showed that sarmentol H had the ability to bind to FXR as a ligand (KD = 2.55 μmol/L) and enhance the stability of its spatial structure. Moreover, site-directed mutagenesis revealed that THR292 and TYR365 were key binding sites for sarmentol H and FXR. Furthermore, knockout of the Fxr gene resulted in a significantly higher degree of ANIT-induced cholestatic liver injury than that in wild-type cholestatic mice, and the amelioration of cholestasis or regulatory effects on FXR downstream genes by sarmentol H also disappeared in Fxr-/- cholestatic mice.

CONCLUSION

Sarmentol H is an FXR agonist. This is the first study to show that it exerts a significant therapeutic effect on cholestatic mice, and can directly bind to FXR and activate it by recruiting the coactivator SRC1.

Multianalytical Approach to Understand Polyphenol-Mal d 1 Interactions to Predict Their Impact on the Allergenic Potential of Apples

Interactions between phenolic compounds and the allergen Mal d 1 are discussed to be the reason for better tolerance of apple cultivars, which are rich in polyphenols. Because Mal d 1 is susceptible to proteolytic digestion and allergenic symptoms are usually restricted to the mouth and throat area, the release of native Mal d 1 during the oral phase is of particular interest. Therefore, we studied the release of Mal d 1 under different in vitro oral digestion conditions and revealed that only 6-15% of the total Mal d 1 present in apples is released. To investigate proposed polyphenol-Mal d 1 interactions, various analytical methods, e.g., isothermal titration calorimetry, 1H-15N-HSQC NMR, and untargeted mass spectrometry, were applied. For monomeric polyphenols, only limited noncovalent interactions were observed, whereas oligomeric polyphenols and browning products caused aggregation. While covalent modifications were not detectable in apple samples, a Michael addition of epicatechin at cysteine 107 in r-Mal d 1.01 was observed.

Recent advances in identifying protein targets of bioactive natural products

Background

Natural products exhibit structural complexity, diversity, and historical therapeutic significance, boasting attractive functions and biological activities that have significantly influenced drug discovery endeavors. The identification of target proteins of active natural compounds is crucial for advancing novel drug innovation. Currently, methods for identifying targets of natural products can be categorized into labeling and label-free approaches based on whether the natural bioactive constituents are modified into active probes. In addition, there is a new avenue for rapidly exploring the targets of natural products based on their innate functions.

Aim

This review aimed to summarize recent advancements in both labeling and label-free approaches to the identification of targets for natural products, as well as the novel target identification method based on the natural functions of natural products.

Methods

We systematically collected relevant articles published in recent years from PubMed, Web of Science, and ScienceDirect, focusing on methods employed for identifying protein targets of bioactive natural products. Furthermore, we systematically summarized the principles, procedures, and successful cases, as well as the advantages and limitations of each method.

Results

Labeling methods allow for the direct labeling of target proteins and the exclusion of indirectly targeted proteins. However, these methods are not suitable for studying post-modified compounds with abolished activity, chemically challenging synthesis, or trace amounts of natural active compounds. Label-free methods can be employed to identify targets of any natural active compounds, including trace amounts and multicomponent mixtures, but their reliability is not as high as labeling methods. The structural complementarity between natural products and their innate receptors significantly increase the opportunities for finding more promising structural analogues of the natural products, and natural products may interact with several structural analogues of receptors in humans.

Conclusion

Each approach presents benefits and drawbacks. In practice, a combination of methods is employed to identify targets of natural products. And natural products' innate functions-based approach is a rapid and selective strategy for target identification. This review provides valuable references for future research in this field, offering insights into techniques and methodologies.

The effects of inulin on solubilizing and improving anti-obesity activity of high polymerization persimmon tannin

High polymerization persimmon tannin has been reported to have lipid-lowering effects. Unfortunately, the poor solubility restricts its application. This research aimed to investigate the effect and mechanism of inulin on solubilizing of persimmon tannin. Furthermore, we examined whether the addition of inulin would affect the attenuated obesity effect of persimmon tannin. Transmission electron microscope (TEM), Isothermal titration calorimetry (ITC) and Fourier transform infrared spectroscopy (FT-IR) results demonstrated that inulin formed a gel-like network structure, which enabled the encapsulation of persimmon tannin through hydrophobic and hydrogen bond interactions, thereby inhibiting the self-aggregation of persimmon tannin. The turbidity of the persimmon tannin solution decreased by 56.2 %, while the polyphenol content in the supernatant increased by 60.0 %. Furthermore, biochemical analysis and 16s rRNA gene sequencing technology demonstrated that persimmon tannin had a significant anti-obesity effect and improved intestinal health in HFD-fed mice. Moreover, inulin was found to have a positive effect on enhancing the health benefits of persimmon tannin, including improving hepatic steatosis and gut microbiota dysbiosis. it enhanced the abundance of beneficial core microbes while decreasing the abundance of harmful bacteria. Our findings expand the applications of persimmon tannin in the food and medical sectors.

Addressing the interaction of stem bromelain with different anionic surfactants, below, at and above the critical micelle concentration (cmc) in phosphate buffer at pH 7: Physicochemical, spectroscopic, & molecular docking study

The structural stability and therapeutic activity of Stem Bromelain (BM) have been explored by unravelling the interaction of stem BM in presence of two different types of anionic surfactants namely, bile salts, NaC and NaDC and the conventional anionic surfactants, SDDS and SDBS, below, at and above the critical micelle concentration (cmc) in aqueous phosphate buffer of pH 7. Different physicochemical parameters like, surface excess (Γcmc), minimum area of surfactants at air water interface (Amin) etc. are calculated from tensiometry both in absence and presence of BM. Several inflection points (C1, C2 and C3) have been found in tensiometry profile of surfactants in presence of BM due to the conformational change of BM assisted by surfactants. Similar observation also found in isothermal titration calorimetry (ITC) profiles where the enthalpy of micellization (ΔH0obs) of surfactants in absence and presence of BM have calculated. Further, steady state absorption and fluorescence spectra monitoring the tryptophan (Trp) emission of free BM and in presence of all the surfactants at three different temperatures (288.15 K, 298.15 K, and 308.15 K) reveal the nature of fluorescence quenching of BM in presence of bile salts/surfactants. Time resolved fluorescence studies at room temperature also support to determine the several quenching parameters. The binding constant (Kb) of BM with all the surfactants and free energy of binding (∆G0 of bile salts/surfactants with BM at different temperatures have been calculated exploiting steady state fluorescence technique. It is observed that, the binding of NaC with BM is greater as compared to other surfactants while Stern-Volmer quenching constant (KSV) is found greater in presence of SDBS as compared with others which supports the surface tension and ITC data with the fact that surface activity of surfactant(s) is decreasing with the binding of the surfactants at the core or binding pocket of BM. Circular Dichroism (CD) study shows the stability of secondary structure of BM in presence of NaC and NaDC below C3, while BM lost its structural stability even at very low surfactant concentration of SDDS and SDBS which also supports the more involvement of bile salts in binding rather than surfactants. The molecular docking studies have also been substantiated for better understanding the several experimental investigations interaction of BM with the bile salts/surfactants.

3-Amide-β-carbolines block the cell cycle by targeting CDK2 and DNA in tumor cells potentially as anti-mitotic agents

β-Carboline alkaloids are natural and synthetic products with outstanding antitumor activity. C3 substituted and dimerized β-carbolines exert excellent antitumor activity. In the present research, 37 β-carboline derivatives were synthesized and characterized. Their cytotoxicity, cell cycle, apoptosis, and CDK2- and DNA-binding affinity were evaluated. β-Carboline monomer M3 and dimer D4 showed selective activity and higher cytotoxicity in tumor cells than in normal cells. Structure-activity relationships (SAR) indicated that the amide group at C3 enhanced the antitumor activity. M3 blocked the A549 (IC50 = 1.44 ± 1.10 μM) cell cycle in the S phase and inhibited A549 cell migration, while D4 blocked the HepG2 (IC50 = 2.84 ± 0.73 μM) cell cycle in the G0/G1 phase, both of which ultimately induced apoptosis. Furthermore, associations of M3 and D4 with CDK2 and DNA were proven by network pharmacology analysis, molecular docking, and western blotting. The expression level of CDK2 was downregulated in M3-treated A549 cells and D4-treated HepG2 cells. Moreover, M3 and D4 interact with DNA and CDK2 at sub-micromolar concentrations in endothermic interactions caused by entropy-driven adsorption processes, which means that the favorable entropy change (ΔS > 0) overcomes the unfavorable enthalpy change (ΔH > 0) and drives the spontaneous reaction (ΔG < 0). Overall, these results clarified the antitumor mechanisms of M3 and D4 through disrupting the cell cycle by binding DNA and CDK2, which demonstrated the potential of M3 and D4 as novel antiproliferative drugs targeting mitosis.

Identifying a New Target for BtOBP8: Discovery of a Small Amino Ketone Molecule Containing Benzothiazole Fragments

Insects rely on odorant-binding proteins (OBPs) for chemical perception, making OBPs a promising target for studying attractants and repellents of pests, such as Bemisia tabaci. However, no reports have reported using B. tabaci OBPs (BtOBPs) as pesticide screening targets. To fill this gap, we obtained BtOBP8 through prokaryotic expression and purification. Then, we confirmed its identity using western blotting and mass spectrometry. Next, we used the sitting drop and hanging drop methods to screen its crystal conditions. Using microscale thermophoresis and isothermal titration calorimetry, we identified the highest affinity ligand, 3l, from 30 compounds. Furthermore, point mutation techniques identified Val119 as a key amino acid residue in binding 31 to BtOBP8. Finally, we tested the bioactivity of B. tabaci Mediterranean and found that 3l more effectively inhibits the bioactivity of B. tabaci MED than imidacloprid. This study presents a new approach for developing green insecticides specific to B. tabaci MED by targeting OBPs. Conclusively, identifying and targeting specific OBPs can create more targeted and effective pest control strategies without relying on toxic chemicals.

Interacting collagen and tannic acid Particles: Uncovering pH-dependent rheological and thermodynamic behaviors

HYPOTHESIS

Biomaterials such as collagen and tannic acid (TA) particles are of interest in the development of advanced hybrid biobased systems due to their beneficial therapeutic functionalities and distinctive structural properties. The presence of numerous functional groups makes both TA and collagen pH responsive, enabling them to interact via non-covalent interactions and offer tunable macroscopic properties.

EXPERIMENT

The effect of pH on the interactions between collagen and TA particles is explored by adding TA particles at physiological pH to collagen at both acidic and neutral pH. Rheology, isothermal titration calorimetry (ITC), turbidimetric analysis and quartz crystal microbalance with dissipation monitoring (QCM-D) are used to study the effects.

FINDINGS

Rheology results show significant increase in elastic modulus with an increase in collagen concentration. However, TA particles at physiological pH provide stronger mechanical reinforcement to collagen at pH 4 than collagen at pH 7 due to the formation of a higher extent of electrostatic interaction and hydrogen bonding. ITC results confirm this hypothesis, with larger changes in enthalpy, |ΔH|, observed when collagen is at acidic pH and |ΔH| > |TΔS| indicating enthalpy-driven collagen-TA interactions. Turbidimetric analysis and QCM-D help to identify structural differences of the collagen-TA complexes and their formation at both pH conditions.

Molecular Editing Enhances Oxidation Resistance of Menaquinone-Targeting Antibiotics Lysocin E and WAP-8294A2

Lysocin E (1 a) and WAP-8294A2 (2 a) are peptidic natural products with 37- and 40-membered macrocycles, respectively. Compounds 1 a and 2 a have potent antibacterial activities against Gram-positive bacteria and share a unique mode of action. The electron-rich indole ring of d-Trp-10 of 1 a and 2 a interacts with the electron-deficient benzoquinone ring of menaquinone, which is a co-enzyme in the bacterial respiratory chain. Formation of the electron-donor-acceptor complex causes membrane disruption, leading to cell death. Despite the promising activities of 1 a and 2 a, the susceptibility of Trp-10 to oxidative degradation potentially deters the development of these compounds as antibacterial drugs. To address this issue, we replaced the indole ring with more oxidation-resistant aromatics having a similar shape and electron-rich character. Specifically, analogues with benzofuran (1 b/2 b), benzothiophene (1 c/2 c), and 1-naphthalene (1 d/2 d) rings were designed, and chemically prepared by full solid-phase total syntheses. Antibacterial assays of the six analogues revealed similar activities of 1 d/2 d and markedly reduced activities of 1 b/2 b and 1 c/2 c compared with 1 a/2 a. Equipotent 1 d and 2 d both showed high resistance to oxidation by peroxyl radicals. Hence, the present study demonstrates a new molecular editing strategy for conferring oxidation stability on natural products with pharmacologically useful functions.

Protective Effect of 20(S)-Protopanaxadiol on D-Gal-Induced Cognitively Impaired Mice Based on Its Target Protein Brain-type Creatine Kinase

Ginseng is an important medicinal herb consumed as dietary supplements. Ginsenosides and their metabolites have been reported to enhance cognitive performance, but their underlying mechanisms remain unclear. Brain-type creatine kinase (CK-BB) was previously screened out as one of the potential targets in brain tissues. In vitro, the strongest direct interaction between 20(S)-protopanaxadiol (PPD), a ginsenoside metabolite, and CK-BB was detected using biolayer interferometry (BLI). Drug affinity responsive target stability, cellular thermal shift assay, BLI, and isothermal titration calorimetry were subsequently used, and the binding of PPD to CK-BB was verified. The binding sites of the CK-BB/PPD complex were clarified by molecular docking and site-directed mutagenesis. Enzyme activity assay showed that the binding of PPD to CK-BB in vitro enhanced its activity. In vivo, PPD increased CK-BB activity in D-gal-induced mice. PPD also improved the D-gal-induced cognitive deficits and ameliorated alterations in oxidative stress and hippocampal synaptic plasticity. Therefore, the integration of PPD with its target protein CK-BB may promote CK-BB activity, thereby ameliorating hippocampal synaptic plasticity and cognitive deficits in D-gal-treated mice.

New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies

In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine²¹⁺ > cohex³⁺ > Ni²⁺ > spermine⁴⁺, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.

A new polysaccharide platform constructs self-adjuvant nanovaccines to enhance immune responses

BACKGROUND

Nanovaccines have shown the promising potential in controlling and eradicating the threat of infectious diseases worldwide. There has been a great need in developing a versatile strategy to conveniently construct diverse types of nanovaccines and induce potent immune responses. To that end, it is critical for obtaining a potent self-adjuvant platform to assemble with different types of antigens into nanovaccines.

RESULTS

In this study, we identified a new natural polysaccharide from the rhizomes of Bletilla striata (PRBS), and used this polysaccharide as a platform to construct diverse types of nanovaccines with potent self-adjuvant property. In the construction process of SARS-CoV-2 nanovaccine, PRBS molecules and RBD protein antigens were assembled into ~ 300 nm nanoparticles by hydrogen bond. For HIV nanovaccine, hydrophobic effect dominantly drove the co-assembly between PRBS molecules and Env expression plasmid into ~ 350 nm nanospheres. Importantly, PRBS can potently activate the behaviors and functions of multiple immune cells such as macrophages, B cells and dendritic cells. Depending on PRBS-mediated immune activation, these self-adjuvant nanovaccines can elicit significantly stronger antigen-specific antibody and cellular responses in vivo, in comparison with their corresponding traditional vaccine forms. Moreover, we also revealed the construction models of PRBS-based nanovaccines by analyzing multiple assembly parameters such as bond energy, bond length and interaction sites.

CONCLUSIONS

PRBS, a newly-identified natural polysaccharide which can co-assemble with different types of antigens and activate multiple critical immune cells, has presented a great potential as a versatile platform to develop potent self-adjuvant nanovaccines.

Bioavailability by design — Vitamin D3 liposomal delivery vehicles

Vitamin D3 deficiency has serious health consequences, as demonstrated by its effect on severity and recovery after COVID-19 infection. Because of high hydrophobicity, its absorption and subsequent redistribution throughout the body are inherently dependent on the accompanying lipids and/or proteins. The effective oral vitamin D₃ formulation should ensure penetration of the mucus layer followed by internalization by competent cells. Isothermal titration calorimetry and computer simulations show that vitamin D₃ molecules cannot leave the hydrophobic environment, indicating that their absorption is predominantly driven by the digestion of the delivery vehicle. In the clinical experiment, liposomal vitamin D₃ was compared to the oily formulation. The results obtained show that liposomal vitamin D₃ causes a rapid increase in the plasma concentration of calcidiol. No such effect was observed when the oily formulation was used. The effect was especially pronounced for people with severe vitamin D₃ deficiency.

Reduced cytotoxicity of nanomaterials driven by nano-bio interactions: Case study of single protein coronas enveloping polymersomes

The protein adsorption onto poly(acrylic acid)-block-polystyrene (PAA₂₂-b-PS₁₄₄) polymersomes has been investigated with regard to structural features, thermodynamic aspects and biological consequences. The light scattering measurements revealed the formation of protein coronas enveloping the polymeric capsules regardless of the chemical nature of the biomacromolecules. The experiments were conducted by using lysozyme, immunoglobulin G - IgG and bovine serum albumin - BSA as model proteins due to their differences concerning size and residual surface charge at physiological pH. The protein adsorption was further confirmed by isothermal titration calorimetry, and the experimental data suggest that the phenomenon is mainly governed by hydrogen bonding and van der Waals interactions. The pre-existing protein layer via the pre-incubation in protein environments notably attenuates the cytotoxicity of the nanomaterial compared to the pristine counterparts. This approach can possibly be extended to different types of assemblies when intermolecular interactions are able to induce protein adsorption and the development of protein coronas around nanoparticles. Such fairly simple method may be convenient to engineer safer nanomaterials towards a variety of biomedical applications when the nanotoxicity is an issue. Additionally, the strategy can possibly be used to tailor the surface properties of nanoparticles by adsorbing specific proteins for targeting purposes.

Identification of Adenylate Kinase 5 as a Protein Target of Ginsenosides in Brain Tissues Using Mass Spectrometry-Based Drug Affinity Responsive Target Stability (DARTS) and Cellular Thermal Shift Assay (CETSA) Techniques

Ginseng is a very famous Chinese herbal medicine with various pharmacological effects. Ginsenosides, the main effective compounds of ginseng, show favorable biological activities in the central nervous system (CNS), but the protein targets of ginsenosides in brain tissues have not been clarified clearly. First, we screened proteins that interact with ginsenosides by mass spectrometry-based drug affinity responsive target stability (DARTS) and cellular thermal shift assay (CETSA). Then, we identified and confirmed adenylate kinase 5 (AK5) as a target protein of ginsenosides by biolayer interferometry (BLI), isothermal titration calorimetry (ITC), and molecular docking. Finally, an enzyme activity kit was used to determine the effect of 20(S)-protopanaxadiol (PPD), a ginseng saponin metabolite, on AK5 activities in vivo and in vitro. We screened out seven overlapping target proteins by proteomics of DARTS and CETSA. The BLI direct action assays showed that the direct interaction of PPD with AK5 was higher compared to the parental ginsenosides. Subsequently, BLI kinetic analysis and ITC assay showed that PPD specifically bound to AK5. Furthermore, key amino acid mutations predicted by molecular docking decreased the affinity between PPD and AK5. Enzyme activity assays showed that PPD increased AK5 activities in vivo and in vitro. The above-mentioned findings indicated that AK5 is a protein target of ginsenoside in the brain and PPD is considered to be a small-molecular activator of AK5, which can improve comprehension of the molecular mechanisms of ginseng pharmacological effects in the CNS and further develop AK5 activators based on the dammarane-type triterpenoid structure.

Assays to Estimate the Binding Affinity of Aptamers

Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.

Methyl 2-Halo-4-Substituted-5-Sulfamoyl-Benzoates as High Affinity and Selective Inhibitors of Carbonic Anhydrase IX

Among the twelve catalytically active carbonic anhydrase isozymes present in the human body, the CAIX is highly overexpressed in various solid tumors. The enzyme acidifies the tumor microenvironment enabling invasion and metastatic processes. Therefore, many attempts have been made to design chemical compounds that would exhibit high affinity and selective binding to CAIX over the remaining eleven catalytically active CA isozymes to limit undesired side effects. It has been postulated that such drugs may have anticancer properties and could be used in tumor treatment. Here we have designed a series of compounds, methyl 5-sulfamoyl-benzoates, which bear a primary sulfonamide group, a well-known marker of CA inhibitors, and determined their affinities for all twelve CA isozymes. Variations of substituents on the benzenesulfonamide ring led to compound 4b, which exhibited an extremely high observed binding affinity to CAIX; the Kd was 0.12 nM. The intrinsic dissociation constant, where the binding-linked protonation reactions have been subtracted, reached 0.08 pM. The compound also exhibited more than 100-fold selectivity over the remaining CA isozymes. The X-ray crystallographic structure of compound 3b bound to CAIX showed the structural position, while several structures of compounds bound to other CA isozymes showed structural reasons for compound selectivity towards CAIX. Since this series of compounds possess physicochemical properties suitable for drugs, they may be developed for anticancer therapeutic purposes.

Modulation of the Protein-Ligand Interaction in the Presence of Graphene Oxide: a Detailed Spectroscopic Study

Several applications of graphene oxide (GO) have been established over the years, and it has the potential to be used as a biomedical material. Studying the effect of GO on protein-ligand (small molecules/drugs) complex systems are vital as the mechanisms involved are not well understood. The interaction of GO on the protein-ligand binding is also vital for the preparation of an effective drug carrier in the bloodstream. In this work, we have tried to explore in details the effect of GO on the interaction between a hydrophilic molecule, namely, 7-(N,N'-diethylamino) coumarin-3-carboxylic acid (7-DCA) with human serum albumin (HSA) by employing multispectroscopic, microscopic, calorimetric, and molecular docking studies. We find out that protein-ligand complexes were placed on the GO surface, and GO gives stability to the protein-ligand complex via hydrogen bonding, electrostatic interactions, hydrophobic interactions, and so forth. Due to the presence of a large surface area in GO, it offers a hydrophobic environment, and as a result, the emission maxima of 7-DCA in the ternary complex is more blue-shifted, and the average lifetime becomes higher compared to the binary system. Circular dichroism spectral studies give information about the conformational changes of HSA in the absence and presence of GO when it forms complex with 7-DCA. The fluorescence lifetime imaging study shows the presence of the 7-DCA/HSA complex on the GO sheet. Molecular docking simulation shows that the closest distance between 7-DCA and HSA is 11.9 Å, and the protein interacted with the ligand through hydrogen bonding, hydrophobic interaction, and so forth.

Uncertainty in protein-ligand binding constants: asymmetric confidence intervals versus standard errors

Equilibrium binding constants (K_b) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reported uncertainties of measured experimental parameters are critical for decision-making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured K_b values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general, the distributions of measured K_b (and equivalent K_d) values and the corresponding free energy change ΔG_b are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric K_b distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of K_b, K_d and ΔG_b are transformed into each other, their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of K_b, K_d, and ΔG_b values is to consistently report 95% confidence intervals, in line with other authors' suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC.

Bean phenolic compound changes during processing: Chemical interactions and identification

The common bean (Phaseolus vulgaris L.) represents one of the main crops for human consumption, due to its nutritional and functional qualities. Phenolic compounds have beneficial health effects, and beans are an essential source of these molecules, being found mainly in the seed coat and its color depends on the concentration and type of phenolic compounds present. The bean during storage and processing, such as cooking, germination, extrusion, and fermentation, undergoes physical, chemical, and structural changes that affect the bioavailability of its nutrients; these changes are related to the interactions between phenolic compounds and other components of the food matrix. This review provides information about the identification and quantification of phenolic compounds present in beans and the changes they undergo during processing. It also includes information on the interactions between the phenolic compounds and the components of the bean's cell wall and the analytical methods used to identify the interactions of phenolic compounds with macromolecules.

Exploring the chemistry behind protein-glycosaminoglycan conjugate: A steady-state and kinetic spectroscopy based approach

The impact of glycosaminoglycan (chondroitin sulphate, CS) on bone morphogenetic protein - 2 (BMP - 2) structure, stability (thermal and chemical), association kinetics and conformation was monitored by multiple spectroscopic techniques (UV-Visible, fluorescence and circular dichroism). The absorbance in peptide region and fluorescence intensity of BMP - 2 was quenched in presence of CS; thus, confirming the formation of a ground-state complex. As there was an increase in Stern-Volmer constant observed as a function of temperature, idea of dynamic quenching was established. However, the negligible changes in lifetime indicated static quenching; thus, making the process a combination of static-dynamic quenching. Basically, the protein - glycan interaction was driven by entropy of the system and mediated by hydrophobic interactions. Secondary structure (CD spectroscopy) of native protein was significantly affected (intensity became more negative) in presence of CS, thus, introducing more compactness in the protein. CS infused thermal and chemical stability into BMP - 2 via alteration in its conformation. The rate of association was inversely proportional to concentration of quencher (CS), which confirmed the correlation between large size (~ 5 times the size of protein) and structural complexity of CS with fewer binding sites present in BMP - 2. The rate of association in presence of urea, suggested a decrease in association rate as a function of urea concentration for 15 μM CS. Experimental evidences suggested an interaction between protein and glycan mediated by hydrophobic interactions, which deciphers structural, thermal and chemical stability into protein.

A novel amorphous solid dispersion based on drug-polymer complexation

Rafoxanide (RAF) is a poorly water-soluble drug that forms a complex with povidone K25 (PVP) in a cosolvent system containing acetone and an alkaline aqueous medium. This study aims to investigate the impact of RAF-PVP complexation on in vitro and in vivo release of RAF. We prepared two RAF amorphous solid dispersions (ASDs) spray-dried from these two cosolvents. The first is a complexation-based spray-drying using a 70% 0.1 N NaOH solution with 30% acetone. The second is a traditional spray-dried formulation containing 80% acetone and 20% ethanol. Evidence from multiple solid-state characterization techniques indicated that ASDs spray-dried using both methods were amorphous. However, RAF ASDs based on drug-polymer complexation in the feed solution demonstrated not only faster drug release during dissolution testing but also higher in vivo absorption in an animal model. The improved RAF release in the complexation-based ASD is due to (1) high energy state of RAF owing to the amorphous form, (2) high pH in the microenvironment due to the ionized state of RAF and residual sodium hydroxide, (3) increased apparent solubility of RAF results from RAF-PVP complexation in dissolution media and biological media, and (4) improved wettability.

Unveiling the Thermodynamic Aspects of Drug-Cyclodextrin Interactions Through Isothermal Titration Calorimetry

Due to their low toxicity and high aqueous solubility, cyclodextrins have emerged as a distinctive class of supramolecules with wide application in the pharmaceutical and food industry. Their ability to improve the water solubility, stability and pharmacokinetic profile of small molecules has established them as a rich toolkit for drug formulation. In order to improve the physicochemical characteristics and the pharmacokinetic profile of a drug through cyclodextrin inclusion, the proper cyclodextrin type has to be selected among the existing great variety consisting of both natural and synthetic variants. The selection of the most proper cyclodextrin variant comes after drug-cyclodextrin screening studies targeting the characterization of the complex formation and evaluation of the affinity and interaction forces participating in the complexation. Numerous analytical, spectroscopic, separation and electrochemical techniques have been applied to elucidate the interaction profile in a cyclodextrin-drug complex. Herein, we describe the application of Isothermal Titration Calorimetry (ITC) on cyclodextrin-drug complexes that enables the charting of the binding affinity and the thermodynamic profile of the inclusion complexes. We focus on the experimental design and present technical tips of the ITC application. To better illustrate the technique's rationale, the interaction between 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) and the antihypertensive drug losartan is investigated.

Synthesis and Stereochemical Assignment of Conioidine A: DNA- and HSA-Binding Studies of the Four Diastereomers

Conioidine A (1), isolated in 1993 with unknown relative and absolute configuration, was suggested to be a DNA-binding compound by an indirect technique. Four stereoisomers of conioidine A have been synthesized from d- and l-proline, and the natural product has been identified as possessing (4R,6R) absolute configuration. Binding of the conioidine diastereomers to calf thymus DNA (CT DNA) and human serum albumin (HSA) has been investigated by fluorescence spectroscopy and isothermal titration calorimetry (ITC). All stereoisomers display at least an order of magnitude weaker binding to DNA than the control compound netropsin; however, a strong association with HSA was observed for the (4R,6S) stereoisomer.

Interactions between cell wall polysaccharides and polyphenols: Effect of molecular internal structure

Cell wall polysaccharides (CPSs) and polyphenols are major constituents of the dietary fiber complex in plant-based foods. Their digestion (by gut microbiota) and bioefficacy depend not only on their structure and quantity, but also on their intermolecular interactions. The composition and structure of these compounds vary with their dietary source (i.e., fruit or vegetable of origin) and can be further modified by food processing. Various components and structures of CPSs and polyphenols have been observed to demonstrate common and characteristic behaviors during interactions. However, at a fundamental level, the mechanisms that ultimately drive these interactions are still not fully understood. This review summarizes the current state of knowledge on the internal factors that influence CPS-polyphenol interactions, describes the different ways in which these interactions can be mediated by molecular composition or structure, and introduces the main methods for the analysis of these interactions, as well as the mechanisms involved. Furthermore, a comprehensive overview is provided of recent key findings in the area of CPS-polyphenol interactions. It is becoming clear that these interactions are shaped by a multitude of factors, the most important of which are the physicochemical properties of the partners: their morphology (surface area and porosity/pore shape), chemical composition (sugar ratio, solubility, and non-sugar components), and molecular architecture (molecular weight, degree of esterification, functional groups, and conformation). An improved understanding of the molecular mechanisms that drive interactions between CPSs and polyphenols may allow us to better establish a bridge between food processing and the bioavailability of colonic fermentation products from CPSs and antioxidant polyphenols, which could ultimately lead to the development of new guidelines for the design of healthier and more nutritious foods.

A molecular understanding of magnesium aluminium silicate - drug, drug - polymer, magnesium aluminium silicate - polymer nanocomposite complex interactions in modulating drug release: Towards zero order release

This study reports the use of ITC in understanding the thermodynamics occurring for a controlled release system in which complexation has been exploited. In this study, a model drug, propranolol hydrochloride (PPN) was complexed with magnesium aluminium silicate (MAS) and these complexes were used in combination with polyethylene oxide (PEO) as a hydrophilic carrier at various concentrations to sustain the release of PPN. DSC, XRPD, ATR-FTIR and SEM/EDX were successfully used in characterising the produced complexes. 2D- SAXS data patterns for MAS and the produced complexes were shown to be symmetric and circular with the particles showing no preferred orientation at the nanometre scale. ITC studies showed differences between PPN adsorption onto MAS compared with PPN adsorption onto a MAS-PEO mixture. At both temperatures studied the binding affinity K_a was greater for the titration of PPN into the MAS-PEO mixture (5.37E + 04 ± 7.54E + 03 M at 25 °C and 8.63E + 04 ± 6.11E + 03 M at 37 °C), compared to the affinity obtained upon binding between PPN and MAS as previously reported suggesting a stronger binding with implications for the dissolution process. MAS-PPN complexes with the PEO polymer compacts displayed desired manufacturing and formulation properties for a formulator including, reduced plastic recovery therefore potentially reducing the risk of cracking/splitting and on tooling wear, controlled release of PPN at a significantly low (5%) polymer level as well as a zero-order release profile (case II transport) using up to 50% polymer level.

Thermodynamics of ferredoxin binding to cyanobacterial nitrate reductase

The role of the seven negatively charged amino acids of Synechocystis sp. PCC 6803 ferredoxin (Fd), i.e., Glu29, Glu30, Asp60, Asp65, Asp66, Glu92, and Glu93, predicted to form complex with nitrate reductase (NR), was investigated using site-directed mutagenesis and isothermal titration calorimetry (ITC). These experiments identified four Fd amino acids, i.e., Glu29, Asp60, Glu92, and Glu93, that are essential for the Fd binding and efficient electron transfer to the NR. ITC measurements showed that the most likely stoichiometry for the wild-type NR/wild-type Fd complex is 1:1, a K_d value 4.7 μM for the complex at low ionic strength residues and both the enthalpic and entropic components are associated with complex formation. ITC titrations of wild-type NR with four Fd variants, E29N, D60N, E92Q, and E93N demonstrated that the complex formation, although favorable, was less energetically favorable when compared to complex formation between the two wild-type proteins, suggesting that these negatively charged Fd residues at these positions are important for the effective and productive interaction with wild-type enzyme.

Combining genetically-encoded biosensors with high throughput strain screening to maximize erythritol production in Yarrowia lipolytica

Erythritol is an important sweetener ingredient and chemical precursor for synthesizing materials with phase transition behavior. Commercial erythritol is primarily produced by industrial fermentation. Further strain engineering necessitates the development of high throughput screening method for rapid detection and screening of mutant strain libraries. In this work, we took advantage of the erythritol-responsive transcription factor EryD, and constructed a sensor-regulator system for rapid screening and characterization of erythritol overproducers. We configured the optimal architecture of the EryD sensor-regulator construct with improved sensitivity, specificity and dynamic response range. Coupled with mutagenesis and strain screening based on biosensors, we rapidly screened and characterized a strain library containing 1152 mutants derived from combined UV and ARTP mutagenesis, in a relatively short period of time (1 week). The optimal strain produced more than 148 g/L erythritol in bench-top reactors. This work provides a reference for other metabolic engineering researchers to develop industrially-relevant strains. The reported framework enables us to rapidly improve strain performance and engineer efficient microbial cell factories for industrial applications.

Molecular mechanism underlying the effects of temperature and pH on the size and surface charge of octenylsuccinated oat β-glucan aggregates

Environmental temperature and pH induced significant changes in the size and surface charge (ζ) of octenylsuccinated oat β-glucan aggregates. The underlying mechanisms were explored by using ¹H-NMR, fluorescence spectra, thermodynamic analysis, and SAXS. At pH 6.5, the size decreased with temperature while ζ continuously increased. With increasing pH at 293 K, parabolic and U-shaped trends were observed in the size and ζ, peaking at pH 8.5 and 6.5, respectively. At any tested pH, the size decreased with temperature. Overall, ζ significantly increased with temperature at each pH. As temperature increased, the compactness of hydrophobic-domains increased while the compactness of hydrophilic-domains decreased. In an acidic environment, both the compactness increased with decreasing pH, but in an alkaline environment, they decreased with pH. The compactness changes were co-driven by enthalpy and entropy and corresponded to changes in the hydrophobic interactions in hydrophobic-domains, hydrogen bonds in hydrophilic-domains and electrostatic repulsions among octenylsuccinate molecules.

Kinetic, Thermodynamic, and Crystallographic Studies of 2-Triazolylthioacetamides as Verona Integron-Encoded Metallo-β-Lactamase 2 (VIM-2) Inhibitor

Inhibition of β-lactamases presents a promising strategy to restore the β-lactams antibacterial activity to resistant bacteria. In this work, we found that aromatic carboxyl substituted 2-triazolylthioacetamides 1a-j inhibited VIM-2, exhibiting an IC50 value in the range of 20.6-58.6 μM. The structure-activity relationship study revealed that replacing the aliphatic carboxylic acid with aromatic carboxyl improved the inhibitory activity of 2-triazolylthioacetamides against VIM-2. 1a-j (16 mg/mL) restored the antibacterial activity of cefazolin against E. coli cell expressing VIM-2, resulting in a 4-8-fold reduction in MICs. The isothermal titration calorimetry (ITC) characterization suggested that the primary binding 2-triazolylthioacetamide (1b, 1c, or 1h) to VIM-2 was a combination of entropy and enthalpy contributions. Further, the crystal structure of VIM-2 in complex with 1b was obtained by co-crystallization with a hanging-drop vapour-diffusion method. The crystal structure analysis revealed that 1b bound to two Zn(II) ions of the enzyme active sites, formed H-bound with Asn233 and structure water molecule, and interacted with the hydrophobic pocket of enzyme activity center utilizing hydrophobic moieties; especially for the phenyl of aromatic carboxyl which formed π-π stacking with active residue His263. These studies confirmed that aromatic carboxyl substituted 2-triazolylthioacetamides are the potent VIM-2 inhibitors scaffold and provided help to further optimize 2-triazolylthioacetamides as VIM-2 even or broad-spectrum MβLs inhibitors.

Real time calorimetric characterisation of clay – drug complex dispersions and particles

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Single loaded and double loaded MAS-PPN complexes successfully made.

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ATR-FTIR confirmed adsorption of PPN onto MAS via hydrogen bonding.

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SEM/EDX showed changes in MAS microstructure upon complexation.

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Drug recovery varied in three media types.

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SIM and MIM experiments showed overall change in enthalpy to be exothermic

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SIM and MIM showed small entropic contribution to the total change in Gibbs free energy.

Isothermal titration calorimetry (ITC) along with attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX) and high-performance liquid chromatography (HPLC) were employed to investigate the process of adsorption of propranolol hydrochloride (PPN) onto magnesium aluminium silicate (MAS) and to characterise the MAS-PPN particles formed upon complexation. The composition of MAS was confirmed by infrared (IR) spectroscopy and a calcimeter. The calorimetric results confirmed the binding between PPN and MAS at various pHs and temperatures. The overall change in enthalpy was found to be exothermic with a comparatively small entropic contribution to the total change in Gibbs free energy. These findings suggest that the binding process was enthalpically driven and entropically unfavourable (lower affinity) suggesting hydrogen bonding and electrostatic interactions dominating the interaction. The variation of pH and temperature did not have a great impact on the thermodynamics of the binding process, as observed from the similarity in enthalpy (ΔH), entropy (ΔS) or Gibbs free energy (ΔG). A slight reduction in the binding affinity (K_a) with varing pH and temperature was however observed. SEM/EDX studies showed the occurrence of changes in the microstructural properties of MAS following complexation which may explain the potential of MAS-PPN complexes for controlled drug release promoting pharmaceutical innovation.

Physicochemical interactions with (-)-epigallocatechin-3-gallate drive structural modification of celiac-associated peptide α2-gliadin (57-89) at physiological conditions

(-)-Epigallocatechin-3-gallate (EGCG), a major phenolic constituent of tea, has been shown to have biological activity within inflammatory pathways involved with food allergies and intolerances. Proposed mechanisms for this effect include sequestration and structural modification of immunostimulatory proteins as a result of interactions with EGCG. The present study employs biophysical techniques including dynamic light scattering, circular dichroism and nuclear magnetic resonance to elucidate the likely mechanism(s) by which EGCG interacts with α2-gliadin (57-89) (α2g), an immunodominant peptide in celiac disease pathogenesis. We demonstrate that EGCG interacts with α2g in a multi-phase reaction driven by non-specific binding, resulting in the formation of polydisperse EGCG/α2g complexes which induce changes in peptide structure. We also show that these interactions occur at a range of pH levels associated with digestion, including pH 2.0, 6.8 and 7.5. Based on previous reports of binding specificity of enzymes and antigen presenting cells in celiac disease pathogenesis, our results provide foundational support for EGCG to prevent recognition of immunostimulatory gliadin epitopes by the body and thus prevent the inflammatory and autoimmune response associated with celiac disease.

Total Synthesis of Alvaradoins E and F, Uveoside, and 10-epi-Uveoside

Concise total syntheses of the anthracenone C-glycosides alvaradoins E and F, uveoside, and 10-epi-uveoside (1-4) have been accomplished from chrysophanic acid 8 and bromosugar 9. Key steps in the syntheses include the DBU-induced coupling of 8 and 9 to produce β-C-glycoside 11, and a Pb(OAc)₄-mediated Kochi reaction to introduce the C-1' oxygen atom of the natural products. Isothermal titration calorimetry and fluorescence binding studies reveal that compounds 1 and 2 have good affinity for the plasma protein HSA.

Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design

The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.

Small molecule target identification using photo-affinity chromatography

Identification of the protein targets of bioactive small molecules is a routine challenge in chemical biology and phenotype-based drug discovery. Recent years have seen an explosion of approaches to meeting this challenge, but the traditional method of affinity pulldowns remains a practical choice in many contexts. This technique can be used as long as an affinity probe can be synthesized, usually with a crosslinking moiety to enable photo-affinity pulldowns. It can be applied to varied tissue types and can be performed with minimal specialized equipment. Here, we provide our protocol for photo-affinity pulldown experiments, with notes on making this method generally applicable to varied target identification challenges.

Protein target identification of ginsenosides in skeletal muscle tissues: discovery of natural small-molecule activators of muscle-type creatine kinase

Background

Ginseng effectively reduces fatigue in both animal models and clinical trials. However, the mechanism of action is not completely understood, and its molecular targets remain largely unknown.

Methods

By screening for proteins that interact with the primary components of ginseng (ginsenosides) in an affinity chromatography assay, we have identified muscle-type creatine kinase (CK-MM) as a potential target in skeletal muscle tissues.

Results

Biolayer interferometry analysis showed that ginsenoside metabolites, instead of parent ginsenosides, had direct interaction with recombinant human CK-MM. Subsequently, 20(S)-protopanaxadiol (PPD), which is a ginsenoside metabolite and displayed the strongest interaction with CK-MM in the study, was selected as a representative to confirm direct binding and its biological importance. Biolayer interferometry kinetics analysis and isothermal titration calorimetry assay demonstrated that PPD specifically bound to human CK-MM. Moreover, the mutation of key amino acids predicted by molecular docking decreased the affinity between PPD and CK-MM. The direct binding activated CK-MM activity in vitro and in vivo, which increased the levels of tissue phosphocreatine and strengthened the function of the creatine kinase/phosphocreatine system in skeletal muscle, thus buffering cellular ATP, delaying exercise-induced lactate accumulation, and improving exercise performance in mice.

Conclusion

Our results suggest a cellular target and an initiating molecular event by which ginseng reduces fatigue. All these findings indicate PPD as a small molecular activator of CK-MM, which can help in further developing better CK-MM activators based on the dammarane-type triterpenoid structure.

Vesicle-Based Assays to Study Membrane Interactions of Amyloid Peptides

The growing interest in membrane interactions of amyloidogenic peptides and proteins emanates from the realization that lipid bilayers and membranes play central roles in the toxicity and pathological pathways of amyloid diseases. This chapter presents experimental schemes designed to study membrane interactions and membrane-induced fibrillation of amyloid peptides.

Real-Time Monitoring of NDM-1 Activity in Live Bacterial Cells by Isothermal Titration Calorimetry: A New Approach To Measure Inhibition of Antibiotic-Resistant Bacteria

The "superbug" infection caused by New Delhi metallo-β-lactamase (NDM-1) has become an emerging threat. Monitoring NDM-1 has proven challenging due to its shuttling between pathogenic bacteria. Here, we report an isothermal titration calorimetry (ITC) method that can monitor activity and inhibition of NDM-1 in live bacterial cells in real time. This method has been exemplified by monitoring of the activity and inhibition of the target enzyme and evaluating the breakdown of antibiotics by pathogenic bacteria expressing β-lactamases. Cell-based studies demonstrate that the NDM-1 expressed in bacterial cells was inhibited by four known inhibitors ethylene diamine tetraacetic acid (EDTA), d-captopril, ebselen and azolylthioacetamide with fifty percent inhibitory concentration (IC₅₀) values of 3.8, 48, 0.55, and 17.5 μM, respectively, which are in good agreement with the data from inhibition kinetics using UV-vis and NMR spectroscopy in vivo. This approach could be applied to screen and evaluate small molecule inhibitors of metallo-β-lactamases (MβLs) in whole cells or to identify drug resistant bacteria.