Fluorescence and Photoacoustic Spectroscopy-Based Assessment of Mitochondrial Dysfunction in Oral Cancer Together with Machine Learning: A Pilot Study

The current study reports an integrated approach of machine learning and tryptophan fluorescence and photoacoustic spectral properties to assess the mitochondrial status under oral pathological conditions. The mitochondria in the study were isolated from oral cancer tissues and adjacent normal counterparts, and the corresponding fluorescence and photoacoustic spectra of tryptophan were recorded at 281 nm pulsed laser excitations. A set of features were selected from the pre-processed spectra and were used to classify the data using support vector machine (SVM) learning in the MATLAB platform. SVM analysis demonstrated clear differentiation between mitochondria isolated from normal and cancer tissues for fluorescence (sensitivity, 86.6%; specificity, 90%) and photoacoustic (sensitivity, 86.6%; specificity, 96.6%) measurements. Further investigation into the influence of change in protein conformation on the nature of tryptophan spectral properties was evaluated by 8-anilino-1-naphthalene sulfonic acid (ANS) fluorescence assay. The impact of protein structural changes on the mitochondrial functions was also estimated by mitochondrial membrane potential (MMP), reactive oxygen species (ROS), and cytochrome c oxidase (COX) assays, suggesting an altered mitochondrial function. The findings indicate that tryptophan fluorescence and photoacoustic spectral properties together with machine learning algorithms may delineate the mitochondrial functional status in vitro, indicating its translational potential.

Characterizing ligand-induced conformational changes in clinically relevant galectin-1 by HN/H2O (D2O) exchange

Glycans of cellular glycoconjugates serve as biochemical signals for a multitude of (patho)physiological processes via binding to their receptors (e.g. lectins). In the case of human adhesion/growth-regulatory galectin-1 (Gal-1), small angle neutron scattering and fluorescence correlation spectroscopy have revealed a significant decrease of its gyration radius and increase of its diffusion coefficient upon binding lactose, posing the pertinent question on the nature and region(s) involved in the underlying structural alterations. Requiring neither a neutron source nor labeling, diffusion measurements by ¹H NMR spectroscopy are shown here to be sufficiently sensitive to detect this ligand-induced change. In order to figure out which region(s) of Gal-1 is (are) affected at the level of peptides, we first explored the use of H/D exchange mass spectrometry (HDX MS). Hereby, we found a reduction in proton exchange kinetics beyond the lactose-binding site. The measurement of fast H^N/H₂O exchange by phase-modulated NMR clean chemical exchange (CLEANEX) NMR on ¹⁵N-labeled Gal-1 then increased the spatial resolution to the level of individual amino acids. The mapped regions with increased protection from H^N/H₂O (D₂O) exchange that include the reduction of solvent exposure around the interface can underlie the protein's compaction. These structural changes have potential to modulate this galectin's role in lattice formation on the cell surface and its interaction(s) with protein(s) at the F-face.

Galectin-Glycan Interactions: Guidelines for Monitoring by 77 Se NMR Spectroscopy, and Solvent (H2 O/D2 O) Impact on Binding

Functional pairing between cellular glycoconjugates and tissue lectins like galectins has wide (patho)physiological significance. Their study is facilitated by nonhydrolysable derivatives of the natural O‐glycans, such as S‐ and Se‐glycosides. The latter enable extensive analyses by specific ⁷⁷Se NMR spectroscopy, but still remain underexplored. By using the example of selenodigalactoside (SeDG) and the human galectin‐1 and ‐3, we have evaluated diverse ⁷⁷Se NMR detection methods and propose selective ¹H,⁷⁷Se heteronuclear Hartmann–Hahn transfer for efficient use in competitive NMR screening against a selenoglycoside spy ligand. By fluorescence anisotropy, circular dichroism, and isothermal titration calorimetry (ITC), we show that the affinity and thermodynamics of SeDG binding by galectins are similar to thiodigalactoside (TDG) and N‐acetyllactosamine (LacNAc), confirming that Se substitution has no major impact. ITC data in D₂O versus H₂O are similar for TDG and LacNAc binding by both galectins, but a solvent effect, indicating solvent rearrangement at the binding site, is hinted at for SeDG and clearly observed for LacNAc dimers with extended chain length.

Facilitated bioreduction of nitrobenzene by lignite acting as low-cost and efficient electron shuttle

The searching for efficient and economical redox mediators to promote the treatment of wastewater containing recalcitrant organic compounds is greatly needed. In this study, the redox mediator activities of four different lignite samples to facilitate the bioreduction of nitrobenzene by Shewanella oneidensis MR-1 were tested for the first time. The initial nitrobenzene reduction rate was increased by 40.4%-90.3% in the presence of 50 mg/L of different lignite samples. Lignite collected from Xinjiang (XJL) having more oxygenated groups performed better in enhancing nitrobenzene bioreduction. The stimulating effects increased with the increase of lignite dosage (0-200 mg/L) and the decrease of lignite particle size (150-0.1 μm). However, the pristine XJL samples with assorted sizes of particles exhibited better stimulating effects than size-fractionated ones, implying that different-sized XJL particles might have synergetic effects on the bioreduction process. When humic acid or iron was removed from XJL, its promoting effects were decreased, demonstrating the crucial roles of both components in lignite-enhanced nitrobenzene bioreduction. Nitric acid treatment could form more oxygenated moieties on lignite surface, which played vital roles in promoting nitrobenzene bioreduction. The initial nitrobenzene bioreduction rate in the presence of HNO₃-treated XJL was 80.8% higher than that obtained with pristine XJL. This study proposed an effective and readily available redox mediator that could be applied to promote the bioreduction of recalcitrant electrophilic pollutants.

Structural basis of the strong cell-cell junction formed by cadherin-23

Cadherin-23, a giant atypical cadherin, forms homophilic interactions at the cell-cell junction of epithelial cells and heterophilic interactions with protocadherin-15 at the tip-links of neuroepithelial cells. While the molecular structure of the heterodimer is solved, the homodimer structure is yet to be resolved. The homodimers play an essential role in cell-cell adhesion as the downregulation of cadherin-23 in cancers loosen the intercellular junction resulting in faster-migration of cancer cells and a significant drop in patient survival. In vitro studies have measured a stronger aggregation-propensity of cadherin-23 compared to typical E-cadherin. Here, we deciphered the unique trans-homodimer structure of cadherin-23 in solution, and show that it consists of two electrostatic-based interfaces extended up to two terminal domains. The interface is robust, with a low off-rate of ~8x10-4 s-1 that supports its strong aggregation-propensity. We identified a point-mutation, E78K, that disrupts this binding. Interestingly, a mutation at the interface was reported in skin cancer. Overall, the structural basis of the strong cadherin-23 adhesion may have far-reaching applications in the fields of mechanobiology and cancer.

Intrinsic tryptophan fluorescence spectroscopy reliably determines galectin-ligand interactions

Galectins are involved in the regulation of divergent physiological and pathological processes and are increasingly recognized to play important roles in a number of diseases. However, a simple and effective way in assessing galectin-ligand interactions is lacking. Our examination of the sequence of all 12 human galectin members reveals the presence of one or more tryptophan residues in the carbohydrate-recognition domains of each galectin. This led us to investigate the possibility that alteration of the galectin intrinsic tryptophan fluorescence could be used in determining the strength of galectin-ligand interactions. One representative member from each of the three subtype galectins, galectin-2 (proto-), galectin-3 (chimera-) and galectin-4 (tandem repeat-type), was selected and analysed for galectin interaction with three ligands of different affinities: galactose, lactose and N-acetyl-lactosamine using tryptophan fluorescence spectroscopy (TFS) and, as a comparison, isothermal titration calorimetry (ITC). Good agreement between TFS and ITC measurements were revealed in ligand bindings of all galectin members. Moreover, TFS detected very weak galectin binding where ITC could not reliably do so. The reliability of TFS in determining galectin-ligand interactions was further validated by analysis of galectin-3 interaction with a semisynthetic ligand, F3. Thus, TFS can be used as a simple, sensitive and reliable way to determine galectin-ligand interactions and also as a drug-discovery platform in developing galectin-targeted therapeutic drugs.

Kinetics of Drug Binding and Residence Time

The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biological target is known as residence time (the inverse of the kinetic constant of the drug-target unbinding, 1/ koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodynamic parameters (free energy, enthalpy, entropy). There are many experimental and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodological approaches to estimating drug binding kinetics and residence time. We first introduce the theoretical background of drug binding kinetics from a physicochemical standpoint. We then analyze the recent literature in the field, starting from the experimental methodologies and applications thereof and moving to theoretical and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of molecular dynamics and related methods, which comprise a great number of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.

Kinetic binding assays for the analysis of protein-ligand interactions

The importance of binding kinetics in terms of residence time and on-rate in drug discovery has been broadly accepted in the past few years. Furthermore, evidence has accumulated that the optimal binding mechanism of a drug to its target molecule is related to physiological efficacy as well as selectivity and thus drug safety. Homogeneous fluorescence-based binding assays have been shown to enable high throughput kinetics requiring only small amounts of protein and can be developed to elucidate even complex mechanisms of molecular recognition. A generalized approach is proposed that combines high quality kinetic and equilibrium data in an Integrated Global Fit analysis yielding the most probable binding mechanism.

Biophysical characterization of lectin–glycan interactions for therapeutics, vaccines and targeted drug-delivery

Lectin–glycan interactions play a role in biological processes, host–pathogen interactions and in disease. A more detailed understanding of these interactions is not only useful for the elucidation of their biological function but can also be applied in immunology, drug development and delivery and diagnostics. We review some commonly used biophysical techniques for studying lectin–glycan interactions; namely: frontal affinity chromatography, glycan/lectin microarray, surface plasmon resonance, electrochemical impedance spectroscopy, isothermal titration calorimetry, fluorescent assays, enzyme linked lectin sorbent assay and saturation transfer difference nuclear magnetic resonance spectroscopy. Each method is evaluated on efficiency, cost and throughput. We also consider the advantages and limitations of each technique and provide examples of their application in biology, drug discovery and delivery, immunology, glycoprofiling and biosensing.

A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code

BACKGROUND

The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts.

SCOPE OF REVIEW

This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching.

MAJOR CONCLUSIONS

The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids.

GENERAL SIGNIFICANCE

Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.

The third dimension of reading the sugar code by lectins: design of glycoclusters with cyclic scaffolds as tools with the aim to define correlations between spatial presentation and activity

Coding of biological information is not confined to nucleic acids and proteins. Endowed with the highest level of structural versatility among biomolecules, the glycan chains of cellular glycoconjugates are well-suited to generate molecular messages/signals in a minimum of space. The sequence and shape of oligosaccharides as well as spatial aspects of multivalent presentation are assumed to underlie the natural specificity/selectivity that cellular glycans have for endogenous lectins. In order to eventually unravel structure-activity profiles cyclic scaffolds have been used as platforms to produce glycoclusters and afford valuable tools. Using adhesion/growth-regulatory galectins and the pan-galectin ligand lactose as a model, emerging insights into the potential of cyclodextrins, cyclic peptides, calixarenes and glycophanes for this purpose are presented herein. The systematic testing of lectin panels with spatially defined ligand presentations can be considered as a biomimetic means to help clarify the mechanisms, which lead to the exquisite accuracy at which endogenous lectins select their physiological counterreceptors from the complexity of the cellular glycome.