Receptor-ligand interactions: Advanced biomedical applications

Stimuli-Responsive Nanomaterials for Tumor Immunotherapy

Cancer remains a significant challenge in extending human life expectancy in the 21st century, with staggering numbers projected by the International Agency for Research on Cancer for upcoming years. While conventional cancer therapies exist, their limitations, in terms of efficacy and side effects, demand the development of novel treatments that selectively target cancer cells. Tumor immunotherapy has emerged as a promising approach, but low response rates and immune-related side effects present significant clinical challenges. Researchers have begun combining immunotherapy with nanomaterials to optimize tumor-killing effects. Stimuli-responsive nanomaterials have become a focus of cancer immunotherapy research due to their unique properties. These nanomaterials target specific signals in the tumor microenvironment, such as pH or temperature changes, to precisely deliver therapeutic agents and minimize damage to healthy tissue. This article reviews the recent developments and clinical applications of endogenous and exogenous stimuli-responsive nanomaterials for tumor immunotherapy, analyzing the advantages and limitations of these materials and highlighting their potential for enhancing the immune response to cancer and improving patient outcomes.

Photothermal driven BMSCs osteogenesis and M2 macrophage polarization on polydopamine-coated Ti3C2 nanosheets/poly(vinylidene fluoride trifluoroethylene) nanocomposite coatings

Mild thermal stimulation plays an active role in bone tissue repair and regeneration. In this work, a bioactive polydopamine/Ti3C2/poly(vinylidene fluoride trifluoroethylene) (PDA/Ti3C2/P(VDF-TrFE)) nanocomposite coating with excellent near-infrared light (NIR)-triggered photothermal effect was designed to improve the osteogenic ability of implants. By incorporating dopamine (DA)-modified Ti3C2 nanosheets into the P(VDF-TrFE) matrix and combining them with alkali initiated in situ polymerization, the resulting PDA/Ti3C2/P(VDF-TrFE) nanocomposite coating gained high adhesion strength on Ti substrate, excellent tribological and corrosion resistance properties, which was quite important for clinical application of implant coatings. Cell biology experiments showed that NIR-triggered mild thermal stimulation on the coating surface promoted cell spreading and growth of BMSCs, and also greatly upregulated the osteogenic markers, including Runt-Related Transcription Factor 2 (RUNX2), alkaline phosphatase (ALP), osteopontin (OPN), osteocalcin (OCN). Simultaneously, the synthesis of heat shock protein 47 (HSP47) was significantly promoted by the mild thermal stimulation, which strengthened the specific interaction between HSP47 and collagen Ⅰ (COL-Ⅰ), thereby activating the integrin-mediated MEK/ERK osteogenic differentiation signaling pathway. In addition, the results also showed that the mild thermal stimulation induced the polarization of macrophages towards M2 phenotype, which can attenuate the inflammatory response of injured bone tissue. Antibacterial results indicated that the coating exhibited an outstanding antibacterial ability against S. aureus and E. coli. Conceivably, the versatile implant bioactive coatings developed in this work will show great application potential for implant osseointegration.

Translocator Protein 18 kDa (TSPO): A Promising Molecular Target for Image-Guided Surgery of Solid Cancers

The translocator protein 18-kDa (TSPO) is a mitochondrial membrane protein that is previously identified as the peripheral benzodiazepine receptor (PBR). Furthermore, it plays a significant role in a diverse range of biochemical processes, including steroidogenesis, mitochondrial cholesterol transport, cell survival and death, cell proliferation, and carcinogenesis. Several investigations also reported its roles in various types of cancers, including colorectal, brain, breast, prostate, and lung cancers, as well as melanoma. According to a previous study, the expression of TSPO was upregulated in cancer cells, which corresponds to an aggressive phenotype and/or poor prognosis. Consequently, the potential for crafting diagnostic and prognostic tools with a focus on TSPO holds great potential. In this context, several radioligands designed to target this protein have been identified, and some of the candidates have advanced to clinical trials. In recent years, the use of hybrid probes with radioactive and fluorescence molecules for image-guided surgery has exhibited promising results in animal and human studies. This indicates that the approach can serve as a valuable surgical navigator during cancer surgery. The current hybrid probes are built from various molecular platforms, including small molecules, nanoparticles, and antibodies. Although several TSPO-targeted imaging probes have been developed, their development for image-guided surgery of cancers is still limited. Therefore, this review aims to highlight recent findings on the involvement of TSPO in carcinogenesis, as well as provide a new perspective on the potential application of TSPO-targeted hybrid probes for image-guided surgery.

Cellular Ligand-Receptor Perturbations Unravel MEIS2 as a Key Factor for the Aggressive Progression and Prognosis in Stage II/III Colorectal Cancer

Approximately 10-15% of stage II and 25-30% of stage III colorectal cancer (CRC) patients experience recurrence within 5 years after surgery, and existing taxonomies are insufficient to meet the needs of clinical precision treatment. Thus, robust biomarkers and precise management were urgently required to stratify stage II and III CRC and identify potential patients who will benefit from postoperative adjuvant therapy. Alongside, interactions of ligand-receptor pairs point to an emerging direction in tumor signaling with far-reaching implications for CRC, while their impact on tumor subtyping has not been elucidated. Herein, based on multiple large-sample multicenter cohorts and perturbations of the ligand-receptor interaction network, four well-characterized ligand-receptor-driven subtypes (LRDS) were established and further validated. These molecular taxonomies perform with unique heterogeneity in terms of molecular characteristics, immune and mutational landscapes, and clinical features. Specifically, MEIS2, a key LRDS4 factor, performs significant associations with proliferation, invasion, migration, and dismal prognosis of stage II/III CRC, revealing promising directions for prognostic assessment and individualized treatment of CRC patients. Overall, our study sheds novel insights into the implications of intercellular communication on stage II/III CRC from a ligand-receptor interactome perspective and revealed MEIS2 as a key factor in the aggressive progression and prognosis for stage II/III CRC.

Deep learning in spatially resolved transcriptfomics: a comprehensive technical view

Spatially resolved transcriptomics (SRT) is a pioneering method for simultaneously studying morphological contexts and gene expression at single-cell precision. Data emerging from SRT are multifaceted, presenting researchers with intricate gene expression matrices, precise spatial details and comprehensive histology visuals. Such rich and intricate datasets, unfortunately, render many conventional methods like traditional machine learning and statistical models ineffective. The unique challenges posed by the specialized nature of SRT data have led the scientific community to explore more sophisticated analytical avenues. Recent trends indicate an increasing reliance on deep learning algorithms, especially in areas such as spatial clustering, identification of spatially variable genes and data alignment tasks. In this manuscript, we provide a rigorous critique of these advanced deep learning methodologies, probing into their merits, limitations and avenues for further refinement. Our in-depth analysis underscores that while the recent innovations in deep learning tailored for SRT have been promising, there remains a substantial potential for enhancement. A crucial area that demands attention is the development of models that can incorporate intricate biological nuances, such as phylogeny-aware processing or in-depth analysis of minuscule histology image segments. Furthermore, addressing challenges like the elimination of batch effects, perfecting data normalization techniques and countering the overdispersion and zero inflation patterns seen in gene expression is pivotal. To support the broader scientific community in their SRT endeavors, we have meticulously assembled a comprehensive directory of readily accessible SRT databases, hoping to serve as a foundation for future research initiatives.

Direct Binding Methods to Measure Receptor-Ligand Interactions

G-protein-coupled receptors (GPCRs) contribute to numerous physiological processes via complex network mechanisms. While indirect signaling assays (Ca2+ mobilization, cAMP production, and GTPγS binding) have been useful in identifying and characterizing downstream signaling mechanisms of GPCRs, these methods lack measurements of direct binding affinities, kinetics, binding specificity, and selectivity that are important parameters in GPCR drug discovery. In comparison to existing direct methods that use radio- or fluorescent labels, label-free techniques can closely emulate the native interactions around binding partners. Surface plasmon resonance (SPR) is a label-free technique that utilizes the refractive index (RI) property and is applied widely in quantitative GPCR-ligand binding kinetics measurement including small molecules screening. However, purified GPCRs are further embedded in a synthetic lipid environment which is immobilized through different tags to the SPR sensor surface, resulting in a non-native environment. Here, we introduced a methodology that also uses the RI property to measure binding interactions in a label-free, immobilization-free arrangement. The free-solution technique is successfully applied in quantifying the interaction of bioactive lipids to cognate lipid GPCRs, which is not purified but rather present in near-native conditions, i.e., in milieu of other cytoplasmic lipids and proteins. To further consider the wide applicability of these free-solution approaches in biomolecular interaction research, additional applications on a variety of receptor-ligand pairs are imperative.

Anxiety in oncology outpatients is associated with perturbations in pathways identified in anxiety focused network pharmacology research

PURPOSE

Evaluate for perturbed signaling pathways associated with subgroups of patients with low versus high levels of state anxiety. These pathways were compared to the pathways identified across eight network pharmacology studies of the anxiolytic effect(s) of a variety of compounds.

METHODS

Adult outpatients had a diagnosis of breast, gastrointestinal, gynecological, or lung cancer; had received chemotherapy within the preceding four weeks; and were scheduled to receive at least two additional cycles of chemotherapy. Latent profile analysis was used to identify subgroups of patients with distinct anxiety profiles based on Spielberger State Anxiety Inventory scores that were obtained six times over two cycles of chemotherapy. Blood samples were processed using RNA sequencing (i.e., RNA-seq sample, n = 244) and microarray (i.e., microarray sample; n = 256) technologies. Pathway perturbations were assessed using pathway impact analysis. Fisher's combined probability method was used to combine test results using a false discovery rate of 0.01.

RESULTS

In the RNA-seq sample, 62.3% and 37.7% of the patients were in the low- and high-anxiety classes, respectively. In the microarray sample, 61.3% and 38.7% were in the low and high-anxiety classes, respectively. Forty-one perturbed signaling pathways were identified. Eight of these pathways were common to those identified in the network pharmacology studies.

CONCLUSIONS

Findings increase our knowledge of the molecular mechanisms that underlie anxiety in patients receiving chemotherapy. This study provides initial insights into how anxiety in patients with cancer may share common mechanisms with anxiety in patients with other clinical conditions.

Surface modification strategies in translocating nano-vesicles across different barriers and the role of bio-vesicles in improving anticancer therapy

Nanovesicles and bio-vesicles (BVs) have emerged as promising tools to achieve targeted cancer therapy due to their ability to overcome many of the key challenges currently being faced with conventional chemotherapy. These challenges include the diverse and often complex pathophysiology involving the progression of cancer, as well as the various biological barriers that circumvent therapeutic molecules reaching their target site in optimum concentration. The scientific evidence suggests that surface-functionalized nanovesicles and BVs camouflaged nano-carriers (NCs) both can bypass the established biological barriers and facilitate fourth-generation targeting for the improved regimen of treatment. In this review, we intend to emphasize the role of surface-functionalized nanovesicles and BVs camouflaged NCs through various approaches that lead to an improved internalization to achieve improved and targeted oncotherapy. We have explored various strategies that have been employed to surface-functionalize and biologically modify these vesicles, including the use of biomolecule functionalized target ligands such as peptides, antibodies, and aptamers, as well as the targeting of specific receptors on cancer cells. Further, the utility of BVs, which are made from the membranes of cells such as mesenchymal stem cells (MSCs), white blood cells (WBCs), red blood cells (RBCs), platelets (PLTs) as well as cancer cells also been investigated. Lastly, we have discussed the translational challenges and limitations that these NCs can encounter and still need to be overcome in order to fully realize the potential of nanovesicles and BVs for targeted cancer therapy. The fundamental challenges that currently prevent successful cancer therapy and the necessity of novel delivery systems are in the offing.

Advancements in portable instruments based on affinity-capture-migration and affinity-capture-separation for use in clinical testing and life science applications

The shift from testing at centralized diagnostic laboratories to remote locations is being driven by the development of point-of-care (POC) instruments and represents a transformative moment in medicine. POC instruments address the need for rapid results that can inform faster therapeutic decisions and interventions. These instruments are especially valuable in the field, such as in an ambulance, or in remote and rural locations. The development of telehealth, enabled by advancements in digital technologies like smartphones and cloud computing, is also aiding in this evolution, allowing medical professionals to provide care remotely, potentially reducing healthcare costs and improving patient longevity. One notable POC device is the lateral flow immunoassay (LFIA), which played a major role in addressing the COVID-19 pandemic due to its ease of use, rapid analysis time, and low cost. However, LFIA tests exhibit relatively low analytical sensitivity and provide semi-quantitative information, indicating either a positive, negative, or inconclusive result, which can be attributed to its one-dimensional format. Immunoaffinity capillary electrophoresis (IACE), on the other hand, offers a two-dimensional format that includes an affinity-capture step of one or more matrix constituents followed by release and electrophoretic separation. The method provides greater analytical sensitivity, and quantitative information, thereby reducing the rate of false positives, false negatives, and inconclusive results. Combining LFIA and IACE technologies can thus provide an effective and economical solution for screening, confirming results, and monitoring patient progress, representing a key strategy in advancing diagnostics in healthcare.

Melanoma molecular subtyping and scoring model construction based on ligand-receptor pairs

Melanoma is a malignancy of melanocytes, responsible for a high percentage of skin cancer mortality. Ligand-Receptor pairs, a type of cellular communication, are essential for tumor genesis, growth, metastasis, and prognosis. Yet, the role of Ligand-Receptor pairs in melanoma has not been fully elucidated. Our research focused on the function of Ligand-Receptor pairs in melanoma prognosis. We screened 131 melanoma prognosis corresponded ligand-receptor pairs by analyzing the TCGA data of melanoma and the 2293 LR pairs retrieved from the connectomeDB2020 database. And further developed subtypes of melanoma according to the expression of these ligand-receptor pairs by Consensus Clustering. Then we using lasso cox regression and stepwise multivariate regression analysis established a ligand-receptor pairs-based scoring model for the evaluation of melanoma prognosis. Our study demonstrated that the ligand-receptor pairs are vital to the molecular heterogeneity of melanoma, and characterized three different melanoma ligand-receptor pairs subtypes. Among them, the C3 subtype showed a better prognosis, while the C1 subtype exhibited a low prognosis state. And our analysis then found out that this could be related to the differed activation and inhabitation of the cell cycle and immune-related pathways. Using lasso cox regression and stepwise multivariate regression analysis, we further identified 9 key ligand-receptor pairs and established a scoring model that effectively correlated with the prognosis, immune pathways, and therapy of melanoma, showing that the LR.score model was a trustworthy and independent biomarker for melanoma prognosis evaluation. In sum, we found that ligand-receptor pairs are significantly associated with the prognosis and therapy of melanoma. And our ligand-receptor-based scoring model showed potential for the evaluation of melanoma prognosis and immune therapy outcome prediction, which is crucial to the survival for the patients.

Crystal Structure Analysis of 4-Oxo, 4-hydroxy- and 4-alkyl-7-bromopyrazolo[5,1-c][1,2,4]triazines

The crystal structures of 8-R1-7-bromo-3-tert-butyl-1-R2-pyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones 1a-c, 2a,c (R1 = CN, CO2Et, NO2, R2 = H, 1:1 and 3:1 solvates with DMSO; R1 = CN, CO2Et, R2 = CH2Boc), 8-R1-7-bromo-3-tert-butyl-1-R2-1,4-dihydropyrazolo[5,1-c][1,2,4]triazin-4-ols 3a,b (R1 = CN, R2 = n-Bu; R1 = Br, R2 = CH2Boc), 1,4-dihydro- and aromatic 7-R3-3-tert-butyl-4-R4-8-methylpyrazolo[5,1-c][1,2,4]triazines 5a,b, 6 (R3 = H, R4 = n-Pr; R3 = Br, R4 = n-Bu) were investigated by X-ray diffraction analysis. The structural preferences and different packing modes based on the intermolecular interactions were analyzed by the Hirshfeld surface and energy framework analysis.

Graphical Abstract

The crystal structures of ten 3-tert-butyl-4-oxo, 4-hydroxy- and 4-alkyl-7-bromopyrazolo[5,1-c][1,2,4]triazines including non-solvated, 1:1 and 3:1 solvates with DMSO were investigated by single crystal X-ray diffraction, Hirshfeld surface and energy framework analyses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10870-022-00973-x.

M, Zarrintaj P, Formela K, Saeb MR, Bencherif SA. Clickable Polysaccharides for Biomedical Applications: A Comprehensive Review

Recent advances in materials science and engineering highlight the importance of designing sophisticated biomaterials with well-defined architectures and tunable properties for emerging biomedical applications. Click chemistry, a powerful method allowing specific and controllable bioorthogonal reactions, has revolutionized our ability to make complex molecular structures with a high level of specificity, selectivity, and yield under mild conditions. These features combined with minimal byproduct formation have enabled the design of a wide range of macromolecular architectures from quick and versatile click reactions. Furthermore, copper-free click chemistry has resulted in a change of paradigm, allowing researchers to perform highly selective chemical reactions in biological environments to further understand the structure and function of cells. In living systems, introducing clickable groups into biomolecules such as polysaccharides (PSA) has been explored as a general approach to conduct medicinal chemistry and potentially help solve healthcare needs. De novo biosynthetic pathways for chemical synthesis have also been exploited and optimized to perform PSA-based bioconjugation inside living cells without interfering with their native processes or functions. This strategy obviates the need for laborious and costly chemical reactions which normally require extensive and time-consuming purification steps. Using these approaches, various PSA-based macromolecules have been manufactured as building blocks for the design of novel biomaterials. Clickable PSA provides a powerful and versatile toolbox for biomaterials scientists and will increasingly play a crucial role in the biomedical field. Specifically, bioclick reactions with PSA have been leveraged for the design of advanced drug delivery systems and minimally invasive injectable hydrogels. In this review article, we have outlined the key aspects and breadth of PSA-derived bioclick reactions as a powerful and versatile toolbox to design advanced polymeric biomaterials for biomedical applications such as molecular imaging, drug delivery, and tissue engineering. Additionally, we have also discussed the past achievements, present developments, and recent trends of clickable PSA-based biomaterials such as 3D printing, as well as their challenges, clinical translatability, and future perspectives.

Activity of arginine-phenylalanine and arginine-tryptophan-based surfactants against Staphylococcus aureus

Aims: This study aimed to evaluate the antibacterial effect of two new cationic surfactants based on phenylalanine-arginine (LPAM) and tryptophan-arginine (LTAM). Materials & methods: Antibacterial activity, mechanism of action and interactions with Staphylococcus aureus enzymes were measured through microbiological, flow cytometry and molecular docking assays, respectively. Results & conclusion: These compounds showed antibacterial activity in the range of 4.06-16.24 μg/ml against planktonic cells and no activity against mature biofilms, since they caused a loss of membrane integrity and increased DNA damage, as revealed by flow cytometry analysis. In silico assays revealed the existence of molecular bonds such as hydrogen bonds, mainly with DNA. Therefore, these compounds have promising pharmacological activity against MRSA strains.

Intercellular communication in the tumour microecosystem: Mediators and therapeutic approaches for hepatocellular carcinoma

Hepatocellular carcinoma (HCC), one of the most common tumours worldwide, is one of the main causes of mortality in cancer patients. There are still numerous problems hindering its early diagnosis, which lead to late patients receiving treatment, and these problems need to be solved urgently. The tumour microecosystem is a complex network system comprising seven parts: the hypoxia niche, immune microenvironment, metabolic microenvironment, acidic niche, innervated niche, mechanical microenvironment, and microbial microenvironment. Intercellular communication is divided into direct contact and indirect communication. Direct contact communication includes gap junctions, tunneling nanotubes, and receptor-ligand interactions, whereas indirect communication includes exosomes, apoptotic vesicles, and soluble factors. Mechanical communication and cytoplasmic exchange are further means of intercellular communication. Intercellular communication mediates the crosstalk between the tumour microecosystem and the host as well as that between cells and cell-free components in the tumour microecosystem, causing changes in the tumour hallmarks of the HCC microecosystem such as changes in tumour proliferation, invasion, apoptosis, angiogenesis, metastasis, inflammatory response, gene mutation, immune escape, metabolic reprogramming, and therapeutic resistance. Here, we review the role of the above-mentioned intercellular communication in the HCC microecosystem and discuss the advantages of targeted intercellular communication in the clinical diagnosis and treatment of HCC. Finally, the current problems and prospects are discussed.

Recent advances in nanomaterials-based optical sensors for detection of various biomarkers (inorganic species, organic and biomolecules)

This review briefly emphasizes the different detection approaches (electrochemical sensors, chemiluminescence, surface-enhanced Raman scattering), functional nanostructure materials (quantum dots, metal nanoparticles, metal nanoclusters, magnetic nanomaterials, metal oxide nanoparticles, polymer-based nanomaterials, and carbonaceous nanomaterials) and detection mechanisms. Further, this review emphasis on the integration of functional nanomaterials with optical spectroscopic techniques for the identification of various biomarkers (nucleic acids, glucose, uric acid, oxytocin, dopamine, ascorbic acid, bilirubin, spermine, serotonin, thiocyanate, Pb²⁺ , Cu²⁺ , Hg²⁺ , F^- , peptides, and cancer biomarkers (mucin 1, prostate specific antigen, carcinoembryonic antigen, CA15-3, human epidermal growth factor receptor 2, C-reactive protein, and interleukin-6). Analytical characteristics of nanomaterials-based optical sensors are summarized in Tables, providing the insights of nanomaterials-based optical sensors for biomarkers detection. Finally, the opportunities and challenges of nanomaterials-based optical analytical approaches for the detection of various biomarkers (inorganic, organic, biomolecules, peptides and proteins) are discussed.

Decorated bacteria and the application in drug delivery

The use of living bacteria either as therapeutic agents or drug carriers has shown great potential in treating a multitude of intractable diseases. However, cells are often fragile to unfriendly environmental stressors and limited by inadequately therapeutic responses, leading to unwanted cell death and a decline in treatment efficacy. Surface decoration of bacteria has emerged as a simple yet useful strategy that not only confers bacteria with extra capacity to resist environmental threats but also endows them with exogenous characteristics that are neither inherent nor naturally achievable. In this review, we systematically introduce the advancements of physicochemical and biological technologies for surface modification of bacteria, especially the single-cell surface decoration strategies of individual bacteria. We highlight the recent progress on surface decoration that aims to improve the bioavailability and efficacy of therapeutic bacterial agents and also to achieve enhanced and targeted delivery of conventional drugs. The promises along with challenges of surface-decorated bacteria as drug delivery systems for applications in cancer therapy, intestinal disease treatment, bioimaging, and diagnosis are further discussed with respect to future clinical translation. This review offers an overview of the advances of decorated bacteria for drug delivery applications and would contribute to the development of the next generation of advanced bacterial-based therapies.

E3 ubiquitin ligase MID1 ubiquitinates and degrades type-I interferon receptor 2

Type I interferon (IFN-I) is a common biological molecule used for the treatment of viral diseases. However, the clinical antiviral efficacy of IFN-I needs to be greatly improved. In this study, IFN-I receptor 2 (IFNAR2) was revealed to undergo degradation at the protein level in cells treated with IFN-I for long periods of time. Further studies found a physical interaction between the E3 ubiquitin ligase Midline-1 (MID1) and IFNAR2. As a consequence, MID1 induced both K48-linked and K63-linked polyubiquitination of IFNAR2, which promoted IFNAR2 protein degradation in a lysosome-dependent manner. Conversely, knockdown of MID1 largely restricted IFN-I-induced degradation of IFNAR2. Importantly, MID1 regulated the strength of IFN-I signaling and IFN-I-induced antiviral activity. These findings reveal a regulatory mechanism of IFNAR2 ubiquitination and protein stability in IFN-I signaling, which could provide a potential target for improving the antiviral efficacy of IFN-I.

3-Thienylboronic Acid as a Receptor for Diol-Containing Compounds: A Study by Isothermal Titration Calorimetry

The electrochemical activity of 3-thienylboronic acid and its feature to form polymer films makes it a perspective receptor material for sensor applications. The affinity properties of this compound were studied here by isothermal titration calorimetry. A number of different analytes were tested, and the highest binding enthalpy was observed for sorbitol and fructose. An increase of pH in the range of 5.5–10.6 results in the rise of the binding enthalpy with an increase of the binding constant to ~8400 L/mol for sorbitol or ~3400 L/mol for fructose. The dependence of the binding constant on pH has an inflection point at pH 7.6 with a slope that is a ten-fold binding constant per one pH unit. The binding properties of 3-thienylboronic acid were evaluated to be very close to that of the phenylboronic acid, but the electrochemical activity of 3-thienylboronic acid provides a possibility of external electrical control: dependence of the affinity of 3-thienylboronic acid on its redox state defined by the presence of ferro/ferricyanide in different ratios was demonstrated. The results show that 3-thienylboronic acid can be applied in smart chemical sensors with electrochemically controllable receptor affinity.

The Study of Protein-Cyclitol Interactions

Investigation of interactions between the target protein molecule and ligand allows for an understanding of the nature of the molecular recognition, functions, and biological activity of protein-ligand complexation. In the present work, non-specific interactions between a model protein (Bovine Serum Albumin) and four cyclitols were investigated. D-sorbitol and adonitol represent the group of linear-structure cyclitols, while shikimic acid and D-(-)-quinic acid have cyclic-structure molecules. Various analytical methods, including chromatographic analysis (HPLC-MS/MS), electrophoretic analysis (SDS-PAGE), spectroscopic analysis (spectrofluorimetry, Fourier transform infrared spectroscopy, and Raman spectroscopy), and isothermal titration calorimetry (ITC), were applied for the description of protein-cyclitol interactions. Additionally, computational calculations were performed to predict the possible binding places. Kinetic studies allowed us to clarify interaction mechanisms that may take place during BSA and cyclitol interaction. The results allow us, among other things, to evaluate the impact of the cyclitol's structure on the character of its interactions with the protein.

Interphase Protein Layers Formed on Self-Assembled Monolayers in Crowded Biological Environments: Analysis by Surface Force and Quartz Crystal Microbalance Measurements

We investigated a viscous protein layer formed on self-assembled monolayers (SAMs) in crowded biological environments. The results were obtained through force spectroscopic measurements using colloidal probes and substantiated by exhaustive analysis using a quartz crystal microbalance with an energy dissipation technique. A hydrophobic SAM of n-octanethiol (C8 SAM) in bovine serum albumin (BSA) solution is buried under an adlayer of denatured BSA molecules and an additional viscous interphase layer that is five times more viscous than the bulk solution. C8 SAMs in fetal bovine serum induced a formation of a thicker adsorbed protein layer but with no observable viscous interphase layer. These findings show that a fouling surface is essentially inaccessible to any approaching molecules and thus has a new biological and physical identity arising from its surrounding protein layers. In contrast, the SAMs composed of sulfobetaine-terminated alkanethiol proved to be sufficiently protein-resistant and bio-inert even under crowded conditions due to a protective barrier of its interfacial water, which has implications in the accurate targeting of artificial particles for drug delivery and similar applications by screening any non-specific interactions. Finally, our strategies provide a platform for the straightforward yet effectual in vitro characterization of diverse types of surfaces in the context of targeted interactions in crowded biological environments.

Peptide Inhibitors of Vascular Endothelial Growth Factor A: Current Situation and Perspectives

Vascular endothelial growth factors (VEGFs) are the family of extracellular signaling proteins involved in the processes of angiogenesis. VEGFA overexpression and altered regulation of VEGFA signaling pathways lead to pathological angiogenesis, which contributes to the progression of various diseases, such as age-related macular degeneration and cancer. Monoclonal antibodies and decoy receptors have been extensively used in the anti-angiogenic therapies for the neutralization of VEGFA. However, multiple side effects, solubility and aggregation issues, and the involvement of compensatory VEGFA-independent pro-angiogenic mechanisms limit the use of the existing VEGFA inhibitors. Short chemically synthesized VEGFA binding peptides are a promising alternative to these full-length proteins. In this review, we summarize anti-VEGFA peptides identified so far and discuss the molecular basis of their inhibitory activity to highlight their pharmacological potential as anti-angiogenic drugs.

Detection of the Chilli Leaf Curl Virus Using an Attenuated Total Reflection-Mediated Localized Surface-Plasmon-Resonance-Based Optical Platform

The development of a nanoparticle-based optical platform has been presented as a biosensor for detecting target-specific plant virus DNA. The binding dynamics of gold nanoparticles has been studied on the amine-functionalized surface by the attenuated total reflection (ATR)-based evanescent wave absorption method monitoring the localized surface plasmon resonance (LSPR). The developed surface was established as a refractive index sensor by monitoring the LSPR absorption peak of gold nanoparticles. This nanoparticle-immobilized surface was explored to establish as a biosensing platform with target-specific immunoglobulin (IgG) antibody-antigen interaction. The IgG concentration-dependent variation of absorbance was correlated with the refractive index change. After successfully establishing this ATR configuration as an LSPR-based biosensor, the single-stranded DNA of the chilli leaf curl virus was detected using its complementary DNA sequence as a receptor. The limit of detection of this sensor was determined to be 1.0 μg/mL for this target viral DNA. This ATR absorption technique has enormous potential as an LSPR based nano-biosensor for the detection of other begomoviruses.

A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine

Over the past decade, traditional Chinese medicine (TCM) has widely embraced systems biology and its various data integration approaches to promote its modernization. Thus, integrative pharmacology-based traditional Chinese medicine (TCMIP) was proposed as a paradigm shift in TCM. This review focuses on the presentation of this novel concept and the main research contents, methodologies and applications of TCMIP. First, TCMIP is an interdisciplinary science that can establish qualitative and quantitative pharmacokinetics-pharmacodynamics (PK-PD) correlations through the integration of knowledge from multiple disciplines and techniques and from different PK-PD processes in vivo. Then, the main research contents of TCMIP are introduced as follows: chemical and ADME/PK profiles of TCM formulas; confirming the three forms of active substances and the three action modes; establishing the qualitative PK-PD correlation; and building the quantitative PK-PD correlations, etc. After that, we summarize the existing data resources, computational models and experimental methods of TCMIP and highlight the urgent establishment of mathematical modeling and experimental methods. Finally, we further discuss the applications of TCMIP for the improvement of TCM quality control, clarification of the molecular mechanisms underlying the actions of TCMs and discovery of potential new drugs, especially TCM-related combination drug discovery.

Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis

MOTIVATION

Ligand-receptor (L-R) interactions mediate cell adhesion, recognition and communication and play essential roles in physiological and pathological signaling. With the rapid development of single-cell RNA sequencing (scRNA-seq) technologies, systematically decoding the intercellular communication network involving L-R interactions has become a focus of research. Therefore, construction of a comprehensive, high-confidence and well-organized resource to retrieve L-R interactions in order to study the functional effects of cell-cell communications would be of great value.

RESULTS

In this study, we developed Cellinker, a manually curated resource of literature-supported L-R interactions that play roles in cell-cell communication. We aimed to provide a useful platform for studies on cell-cell communication mediated by L-R interactions. The current version of Cellinker documents over 3,700 human and 3,200 mouse L-R protein-protein interactions (PPIs) and embeds a practical and convenient webserver with which researchers can decode intercellular communications based on scRNA-seq data. And over 400 endogenous small molecule (sMOL) related L-R interactions were collected as well. Moreover, to help with research on coronavirus (CoV) infection, Cellinker collects information on 16 L-R PPIs involved in CoV-human interactions (including 12 L-R PPIs involved in SARS-CoV-2 infection). In summary, Cellinker provides a user-friendly interface for querying, browsing and visualizing L-R interactions as well as a practical and convenient web tool for inferring intercellular communications based on scRNA-seq data. We believe this platform could promote intercellular communication research and accelerate the development of related algorithms for scRNA-seq studies.

AVAILABILITY

Cellinker is available at http://www.rna-society.org/cellinker/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Enhanced cellular osteogenic differentiation on CoFe2O4/P(VDF-TrFE) nanocomposite coatings under static magnetic field

Cellular responses can be regulated and manipulated through combining stimuli-responsive biomaterial with external stimulus. In this present, the magneto-responsive CoFe₂O₄/P(VDF-TrFE) nanocomposite coatings were designed to understand cell behaviors of preosteoblasts, as well as get insight into the underlying mechanism of osteogenic differentiation under static magnetic field (SMF). CoFe₂O₄/P(VDF-TrFE) nanocomposite coatings with differential magnetic property (low, medium and high magnetization) were prepared by incorporation of different mass fraction of CoFe₂O₄ nanoparticles (6%, 13 %, 20 %) into P(VDF-TrFE) matrix. Cell experiments indicated that all nanocomposite coatings with the assistance of SMF could promote the cell attachment, proliferation and osteogenic differentiation of MC3T3-E1 cells. Among different nanocomposite coatings, low magnetization coating (6%) showed a higher ALP activity and gene expression of Runx2, Col-I, OCN. Molecular biology assays demonstrated that the combination of nanocomposite coatings and SMF could significantly up-regulate the expression level of α2β1 integrin and p-ERK. Whereas, the addition of inhibitor U0126 down-regulated sharply the expression level of p-ERK, which indicated that cellular osteogenic differentiation of MC3T3-E1 cells was governed through α2β1 integrin-mediated MEK/ERK signaling pathways during CoFe₂O₄/P(VDF-TrFE) nanocomposite coatings were combined with SMF. This work provided a promising strategy to enhance cellular osteogenic differentiation through a remote-control manner, which exhibited great potential in the application of bone tissue repair and regeneration.

Endothelial Glycocalyx-Mediated Intercellular Interactions: Mechanisms and Implications for Atherosclerosis and Cancer Metastasis

Purpose

The endothelial glycocalyx (GCX) plays a critical role in the health of the vascular system. Degradation of the GCX has been implicated in the onset of diseases like atherosclerosis and cancer because it disrupts endothelial cell (EC) function that is meant to protect from atherosclerosis and cancer. Examples of such EC function include interendothelial cell communication via gap junctions and receptor-mediated interactions between endothelial and tumor cells. This review focuses on GCX-dependent regulation of these intercellular interactions in healthy and diseased states. The ultimate goal is to build new knowledge that can be applied to developing GCX regeneration strategies that can control intercellular interaction in order to combat the progression of diseases such as atherosclerosis and cancer.

Methods

In vitro and in vivo studies were conducted to determine the baseline expression of GCX in physiologically relevant conditions. Chemical and mechanical GCX degradation approaches were employed to degrade the GCX. The impact of intact versus degraded GCX on intercellular interactions was assessed using cytochemistry, histochemistry, a Lucifer yellow dye transfer assay, and confocal, intravital, and scanning electron microscopy techniques.

Results

Relevant to atherosclerosis, we found that GCX stability determines the expression and functionality of Cx43 in gap junction-mediated EC-to-EC communication. Relevant to cancer metastasis, we found that destabilizing the GCX through either disturbed flow-induced or enzyme induced GCX degradation results in increased E-selectin receptor-mediated EC-tumor cell interactions.

Conclusion

Our findings lay a foundation for future endothelial GCX-targeted therapy, to control intercellular interactions and limit the progression of atherosclerosis and cancer.

Study on FcγRn Electrochemical Receptor Sensor and Its Kinetics

Neonatal γ-immunoglobulin (IgG) Fc receptor (FcγRn) is a receptor that transports IgG across the intestinal mucosa, placenta, and mammary gland, ensuring the balance of IgG and albumin in the body. These functions of FcγRn depend on the intracellular signal transduction and activation caused by the combination of its extracellular domain and IgG Fc domain. Nevertheless, there are still no kinetic studies on this interaction. Consequently, in the present study, we successfully constructed the human FcγRn (hFcγRn) electrochemical receptor sensor. The signal amplification system formed by chitosan nanogold-hFcγRn protein and horseradish peroxidase was used to simulate the cell signal amplification system in vivo, and the kinetic effects between seven IgG and hFcγRn receptors from different species were quantitatively measured. The results showed that the interaction of these seven IgGs with hFcγRn was similar to the catalytic kinetics of enzyme and substrate, and there was a ligand-receptor saturation effect. The order of the interconnect allosteric constants (Ka), which is similar to the Michaelis constant (Km), was human IgG < bovine IgG < horse IgG < rabbit IgG < sheep IgG < donkey IgG < quail IgY. The results showed that hFcγRn had the strongest ability to transport human IgG, which was consistent with the evolution of the system. Therefore, our hFcγRn electrochemical receptor sensor can be used to measure and evaluate the interconnected allosteric network. It is also an essential parameter of the interaction between hFcγRn and different IgGs and, thus, provides a new detection and evaluation method for immunoemulsion, therapeutic monoclonal antibody therapy, heteroantibody treatment, and half-life research.

Molecular modeling of a series of dehydroquinate dehydratase type II inhibitors of Mycobacterium tuberculosis and design of new binders

Tuberculosis, caused by Mycobacterium tuberculosis (M. tuberculosis), is still responsible for a large number of fatal cases, especially in developing countries with alarming rates of incidence and prevalence worldwide. Mycobacterium tuberculosis has a remarkable ability to develop new resistance mechanisms to the conventional antimicrobials treatment. Because of this, there is an urgent need for novel bioactive compounds for its treatment. The dehydroquinate dehydratase II (DHQase II) is considered a key enzyme of shikimate pathway, and it can be used as a promising target for the design of new bioactive compounds with antibacterial action. The aim of this work was the construction of QSAR models to aid the design of new potential DHQase II inhibitors. For that purpose, various molecular modeling approaches, such as activity cliff, QSAR models and computer-aided ligand design were utilized. A predictive in silico 4D-QSAR model was built using a database comprising 86 inhibitors of DHQase II, and the model was used to predict the activity of the designed ligands. The obtained model proved to predict well the DHQase II inhibition for an external validation dataset ([Formula: see text] = 0.72). Also, the Activity Cliff analysis shed light on important structural features applied to the ligand design.

Modeling interaction between gp120 HIV protein and CCR5 receptor

The study of the process of HIV entry into the host cell and the creation of biomimetic nanosystems that are able to selectively bind viral particles and proteins is a high priority research area for the development of novel diagnostic tools and treatment of HIV infection. Recently, we described multilayer nanoparticles (nanotraps) with heparin surface and cationic peptides comprising the N-terminal tail (Nt) and the second extracellular loop (ECL2) of CCR5 receptor, which could bind with high affinity some inflammatory chemokines, in particular, Rantes. Because of the similarity of the binding determinants in CCR5 structure, both for chemokines and gp120 HIV protein, here we expand this approach to the study of the interactions of these biomimetic nanosystems and their components with the peptide representing the V3 loop of the activated form of gp120. According to surface plasmon resonance results, a conformational rearrangement is involved in the process of V3 and CCR5 fragments binding. As in the case of Rantes, ECL2 peptide showed much higher affinity to V3 peptide than Nt (K_D  = 3.72 × 10^-8 and 1.10 × 10^-6  M, respectively). Heparin-covered nanoparticles bearing CCR5 peptides effectively bound V3 as well. The presence of both heparin and the peptides in the structure of the nanotraps was shown to be crucial for the interaction with the V3 loop. Thus, short cationic peptides ECL2 and Nt proved to be excellent candidates for the design of CCR5 receptor mimetics.

Novel Pathway for Efficient Covalent Modification of Polyester Materials of Different Design to Prepare Biomimetic Surfaces

To form modern materials with biomimic surfaces, the novel pathway for surface functionalization with specific ligands of well-known and widely used polyester-based rigid media was developed and optimized. Two types of material bases, namely, poly(lactic acid) and poly(ε-caprolactone), as well as two types of material design, e.g., supermacroporous matrices and nanoparticles (NPs), were modified via covalent attachment of preliminary oxidized polyvinylsaccharide poly(2-deoxy-N-methacryloylamido-d-glucose) (PMAG). This polymer, being highly biocompatible and bioinspired, was used to enhance hydrophilicity of the polymer surface and to provide the elevated concentration of reactive groups required for covalent binding of bioligands of choice. The specialties of the interaction of PMAG and its preliminary formed bioconjugates with a chemically activated polyester surface were studied and thoroughly discussed. The supermacroporous materials modified with cell adhesion motifs and Arg-Gly-Asp-containing peptide (RGD-peptide) were tested in the experiments on bone tissue engineering. In turn, the NPs were modified with bioligands ("self-peptide" or camel antibodies) to control their phagocytosis that can be important, for example, for the preparation of drug delivery systems.

Perspectives on the past, present, and future of cancer nanomedicine

The justification of cancer nanomedicine relies on enhanced permeation (EP) and retention (R) effect and the capability of intracellular targeting due primarily to size after internalization (endocytosis) into the individual target cells. The EPR effect implies improved efficacy. Affinity targeting for solid tumors only occur after delivery to individual cells, which help internalization and/or retention. The design principles have been supported by animal results in numerous publications, but hardly translated. The natures of EP and R, such as frequency of large openings in tumor vasculature and their dynamics, are not understood, in particular, in clinical settings. Although various attempts to address the issues related to EP and delivery, by modifying design factors and manipulating tumor microenvironment, are being reported, they are still verified in artificial rodent tumors which do not mimic the nature of human tumor physiology/pathology in terms of transport and delivery. The clinical trials of experimental nanomedicine have experienced unexpected adverse effects with modest improvement in efficacy when compared to current frontline therapy. Future nanomedicine may require new design principles without consideration of EP and affinity targeting. A possible direction is to set new approaches to intentionally minimize adverse effects, rather than aiming at better efficacy, which can widen the therapeutic window of an anticancer drug of interest. Broadening indications and administration routes of developed therapeutic nanotechnology would benefit patients.

Structure-based design and application of a nucleotide coenzyme mimetic ligand: Application to the affinity purification of nucleotide dependent enzymes

In the present study, a structure-based approach was exploited for the in silico design of a nucleotide coenzyme mimetic ligand. The enzyme formate dehydrogenase (FDH) was employed as a model in our study. The biomimetic ligand was designed and synthesized based on a tryptamine/3-aminopropylphosphonic acid bi-substituted 1,3,5-triazine (Trz) scaffold (Tra-Trz-3APP), which potentially mimics the interactions of NAD⁺-FDH complex. Molecular docking studies of the biomimetic ligand predicted that it can occupy the same binding site as the natural coenzyme. Molecular modeling and dynamics simulations revealed that the ligand binds in an energetically more stable pose in the FDH binding site, as it adopts a more twisty conformation, compared to the natural coenzyme. Study of the FDH/Tra-Trz-3APP-Sepharose interaction, through adsorption equilibrium studies and site-directed mutagenesis of selected FDH coenzyme binding residues, provided additional experimental evidences of the specificity of the interaction. The Tra-Trz-3APP-Sepharose biomimetic adsorbent was further evaluated towards a range of different dehydrogenases and was exploited for the development of a single-step purification protocol for FDH. The protocol afforded enzyme with high yield and purity, suitable for analytical and industrial purposes.

Molecularly imprinted polymers as receptor mimics for selective cell recognition

Molecularly imprinted polymers are now approaching the perfection of natural receptors, e.g., the ability to interact with or recognize cells.

Amphiphilic polypeptides with prolonged enzymatic stability for the preparation of self-assembled nanobiomaterials

Aib residue distribution in Lys/Aib polymers influences the morphology of forming nanoparticles and the rate of their enzymatic degradation.