Specific Ligands Research Articles

Single-Nucleotide Polymorphisms of TAS2R46 Affect the Receptor Downstream Calcium Regulation in Histamine-Challenged Cells.

Bitter taste receptors (TAS2Rs) expressed in extraoral tissues represent a whole-body sensory system, whose role and mechanisms could be of interest for the identification of new therapeutic targets. It is known that TAS2R46s in pre-contracted airway smooth muscle cells increase mitochondrial calcium uptake, leading to bronchodilation, and that several SNPs have been identified in its gene sequence. There are very few reports on the structure-function analysis of TAS2Rs. Thus, we delved into the subject by using mutagenesis and in silico studies. We generated a cellular model that expresses native TAS2R46 to evaluate the influence of the four most common SNPs on calcium fluxes following the activation of the receptor by its specific ligand absinthin. Then, docking studies were conducted to correlate the calcium flux results to the structural mutation. The analysed SNPs differently modulate the TAS2R46 signal cascade according to the altered protein domain. In particular, the SNP in the sixth transmembrane domain of the receptors did not modulate calcium homeostasis, while the SNPs in the sequence coding for the fourth transmembrane domain completely abolished the mitochondrial calcium uptake. In conclusion, these results indicate the fourth transmembrane domain of TAS2R46 is critical for the intrinsic receptor activity.

Nuclear receptors in ovarian cancer: changing paradigms in cancer therapeutics.

Ovarian cancer (OVC) is one of the most common causes of cancer-related deaths in women worldwide. Despite advancements in detection and therapy, the prognosis of OVC remains poor due to late diagnosis and the lack of effective therapeutic options at advanced stages. Therefore, a better understanding of the biology underlying OVC is essential for the development of effective strategies for early detection and targeted therapies. Nuclear receptors (NRs) are a superfamily of 48 transcription factors that, upon binding to their specific ligand, play a vital role in regulating various cellular processes such as growth, development, metabolism, and homeostasis. Accumulating evidence from several studies has shown that their aberrant expression is associated with multiple human diseases. Numerous NRs have shown significant effects in the development of various cancers, including OVC. This review summarizes the recent findings on the role of NRs in OVC, as well as their potential as prognostic and therapeutic markers. Further, the basic structure and signaling mechanism of NRs have also been discussed briefly. Moreover, this review highlights their cellular and molecular mechanisms in chemoresistance and chemosensitization. Further, the clinical trials targeting NRs for the treatment of OVC have also been discussed.

Lighting and rapid detection of the Coronavirus S protein using computationally speculated ligand and its application in SARS-CoV-2

Detection of key proteins has enormous medical potential, particularly during the initial phase of an outbreak of infectious diseases. For this purpose, we develop a research paradigm based on computational speculation. With the rapid development of computers, it is possible to analyze the structure of key proteins and screen specific fluorescent ligands through computational tools. This process resembles the production of antibodies but is more effective, and the resultant product is significantly cheaper. A proof of concept was demonstrated by studying the S protein of SARS-CoV-2. The structural data of the S protein enabled automated docking with fluorescent molecules. After two rounds of conditional screening and verification, the most effective fluorescent ligand, Protoporphyrin IX (PPIX), was identified. PPIX illuminates the S protein, recovers fluorescence upon binding. The illuminated complex is enriched by a single microsphere, allowing for the quantitative analysis of the proteins through fluorescence intensity. Finally, less than 1000 copies S protein-bearing pseudovirus can be detected in 20 minutes without amplification. Overall, we established a highly sensitive general method for protein detection based on single microsphere enrichment with the aid of computerised simulation. We hope this integrated approach will provide new insights for rapid screening in epidemic populations.

Low-Temperature Catalytic Transfer Hydrogenation of Biomass-Derived Furfural over Irreversibly Adsorbed and Highly Dispersed Zr(IV) Species.

Developing pure inorganic catalysts for low-energy transfer hydrogenation of biomass-derived furfural and alcohols below 100 °C is still challenging. This work reports highly dispersed Zr(IV) species catalysts prepared by irreversible adsorption of different solvent-dissolved Zr(IV) cations such as Zr4+ or [Zr4(OH)8(H2O)16]8+ on/in SBA-15 through Zr-O coordination, without adding an alkaline precipitant and calcination treatment. In the transfer hydrogenation of furfural to furfuryl alcohol, the Zr(IV) species catalysts exhibited unexpectedly outstanding transfer hydrogenation activity at low temperatures of 70 and 85 °C, superior to other transition-metal (Zr4+, Hf4+, Fe3+, etc.)- and main-group metal (Al3+, etc.)-based inorganic catalysts, which need high reaction temperatures above 100 °C, and comparable to the best-performing metal-organic hybrid catalysts with precise defect engineering modification or specific macromolecular ligands, and had negligible Zr leaching amounts (<0.01%) in water and in the collected liquid reaction medium from 7 cycles of reactions. In addition, the large strong Lewis acidic site amount rather than the large total acidic amount is a crucial condition for the catalysts to obtain high transfer hydrogenation activity, and basic sites were also involved in catalysis, and their absence would induce the acetalization side reaction. Furthermore, the catalysts were universal for low-temperature transfer hydrogenation of other aldehydes.

HLA and KIR genetic association and NK cells in anti-NMDAR encephalitis.

Genetic predisposition to autoimmune encephalitis with antibodies against N-methyl-D-aspartate receptor (NMDAR) is poorly understood. Given the diversity of associated environmental factors (tumors, infections), we hypothesized that human leukocyte antigen (HLA) and killer-cell immunoglobulin-like receptors (KIR), two extremely polymorphic gene complexes key to the immune system, might be relevant for the genetic predisposition to anti-NMDAR encephalitis. Notably, KIR are chiefly expressed by Natural Killer (NK) cells, recognize distinct HLA class I allotypes and play a major role in anti-tumor and anti-infection responses. We conducted a Genome Wide Association Study (GWAS) with subsequent control-matching using Principal Component Analysis (PCA) and HLA imputation, in a multi-ethnic cohort of anti-NMDAR encephalitis (n=479); KIR and HLA were further sequenced in a large subsample (n=323). PCA-controlled logistic regression was then conducted for carrier frequencies (HLA and KIR) and copy number variation (KIR). HLA-KIR interaction associations were also modeled. Additionally, single cell sequencing was conducted in peripheral blood mononuclear cells from 16 cases and 16 controls, NK cells were sorted and phenotyped. Anti-NMDAR encephalitis showed a weak HLA association with DRB1*01:01~DQA1*01:01~DQB1*05:01 (OR=1.57, 1.51, 1.45; respectively), and DRB1*11:01 (OR=1.60); these effects were stronger in European descendants and in patients without an underlying ovarian teratoma. More interestingly, we found increased copy number variation of KIR2DL5B (OR=1.72), principally due to an overrepresentation of KIR2DL5B*00201. Further, we identified two allele associations in framework genes, KIR2DL4*00103 (25.4% vs. 12.5% in controls, OR=1.98) and KIR3DL3*00302 (5.3% vs. 1.3%, OR=4.44). Notably, the ligands of these KIR2DL4 and KIR3DL3, respectively, HLA-G and HHLA2, are known to act as immune checkpoint with immunosuppressive functions. However, we did not find differences in specific KIR-HLA ligand interactions or HLA-G polymorphisms between cases and controls. Similarly, gene expression of CD56dim or CD56bright NK cells did not differ between cases and controls. Our observations for the first time suggest that the HLA-KIR axis might be involved in anti-NMDAR encephalitis. While the genetic risk conferred by the identified polymorphisms appears small, a role of this axis in the pathophysiology of this disease appears highly plausible and should be analyzed in future studies.

The careful selection of zwitterionic nanoparticle coating results in rapid and efficient cell labeling for imaging‐based cell tracking

AbstractThe increased clinical application of cell‐based therapies has resulted in a parallel increase in the need for non‐invasive imaging‐based approaches for cell tracking, often through labeling with nanoparticles. An ideal nanoparticle for such applications must be biologically compatible as well as readily internalized by cells to ensure adequate and stable cell loading. Surface coatings have been used to make nanoparticle trackers suitable for these purposes, but those currently employed tend to have cytotoxic effects. Zwitterionic ligands are known to be biocompatible and antifouling; however, head‐to‐head evaluation of specific zwitterionic ligands for cell loading has not yet been explored. Magnetic particle imaging (MPI) detects superparamagnetic iron oxide nanoparticles (SPIONs) using time‐varying magnetic fields. Because MPI can produce high‐contrast, real‐time images with no tissue depth limitation, it is an ideal candidate for in vivo cell tracking. In this work, we have conjugated hard (permanently charged) and soft (pKa‐dependently charged) biomimetic zwitterionic ligands to SPIONs and characterized how these ligands changed SPION physicochemical properties. We have evaluated cellular uptake and subcellular localization between zwitterions, how the improvement in cell uptake generated stronger MPI signal for smaller numbers of cells, and how these cells can be tracked in an animal model with greater sensitivity for longer periods of time. Our best‐performing surface coating afforded high cell loading within 4 h, with full signal retention in vivo over 7 days.

TLR Agonists Modify NK Cell Activation and Increase Its Cytotoxicity in Acute Lymphoblastic Leukemia.

Natural killer (NK) cells play a crucial role in innate immunity, particularly in combating infections and tumors. However, in hematological cancers, NK cells often exhibit impaired functions. Therefore, it is very important to activate its endosomal Toll-like receptors (TLRs) as a potential strategy to restore its antitumor activity. We stimulated NK cells from the peripheral blood mononuclear cells from children with acute lymphoblastic leukemia and NK cells isolated, and the NK cells were stimulated with specific TLR ligands (Poly I:C, Imiquimod, R848, and ODN2006) and we evaluated changes in IFN-γ, CD107a, NKG2D, NKp44 expression, Granzyme B secretion, cytokine/chemokine release, and cytotoxic activity. Results revealed that Poly I:C and Imiquimod enhanced the activation of both immunoregulatory and cytotoxic NK cells, increasing IFN-γ, CD107a, NKG2D, and NKp44 expression. R848 activated immunoregulatory NK cells, while ODN2006 boosted CD107a, NKp44, NKG2D, and IFN-γ secretion in cytotoxic NK cells. R848 also increased the secretion of seven cytokines/chemokines. Importantly, R848 and ODN 2006 significantly improved cytotoxicity against leukemic cells. Overall, TLR stimulation enhances NK cell activation, suggesting TLR8 (R848) and TLR9 (ODN 2006) ligands as promising candidates for antitumor immunotherapy.

Synergistic Targeting of Innate Receptors TLR7 and NOD2 for Therapeutic Intervention in Multiple Sclerosis.

Regulation of neuroinflammation is critical for maintaining central nervous system (CNS) homeostasis and holds therapeutic promise in autoimmune diseases such as multiple sclerosis (MS). Previous studies have highlighted the significance of selective innate signaling in triggering anti-inflammatory mechanisms, which play a protective role in an MS-like disease, experimental autoimmune encephalomyelitis (EAE). However, the individual intra-CNS administration of specific innate receptor ligands or agonists, such as for toll-like receptor 7 (TLR7) and nucleotide-binding oligomerization-domain-containing protein 2 (NOD2), failed to elicit the desired anti-inflammatory response in EAE. In this study, we investigated the potential synergistic effect of targeting both TLR7 and NOD2 simultaneously to prevent EAE progression. Our findings demonstrate that simultaneous intrathecal administration of NOD2- and TLR7-agonists led to synergistic induction of Type I IFN (IFN I) and effectively suppressed EAE in an IFN I-dependent manner. Suppression of EAE was correlated with a significant decrease in the infiltration of monocytes, granulocytes, and natural killer cells, reduced demyelination, and downregulation of IL-1β, CCL2, and IFNγ gene expression in the spinal cord. These results underscore the therapeutic promise of concurrently targeting the TLR7 and NOD2 pathways in alleviating neuroinflammation associated with MS, paving the way for novel and more efficacious treatment strategies.

Friction between a single platelet and fibrinogen

Friction has been considered to mediate physiological activities of cells, however, the biological friction between a single cell and its ligand-bound surface has not been thoroughly explored. Herein, we established a friction model for single cells based on an atomic force microscopy (AFM) combined with an inverted fluorescence microscopy (IFM) to study the friction between a highly sensitive platelet and fibrinogen-coated surface. The study revealed that the friction between the platelet and fibrinogen-coated tip is mainly influenced by specific ligand–receptor interaction. Further, we modeled the biological friction, which consists of specific interaction, non-specific interaction, and mechanical effect. Besides, the results suggested that the velocity can also affect specific ligand–receptor interactions, resulting in the friction change and platelet adhesion to fibrinogen surfaces. The study built a friction model between a single cell and its ligand-bound surface and provided a potential method to study the biological friction by the combination of AFM and IFM.

Cooperative binding of bivalent ligands yields new insights into the guanidine-II riboswitch.

Riboswitches are involved in regulating the gene expression in bacteria. They are located within the untranslated regions of bacterial messenger RNA and function as switches by adjusting their shape, depending on the presence or absence of specific ligands. To decipher the fundamental aspects of bacterial gene control, it is therefore important to understand the mechanisms that underlie these conformational switches. To this end, a combination of an experimental binding study, molecular simulations and machine learning has been employed to obtain insights into the conformational changes and structural dynamics of the guanidine-II riboswitch. By exploiting the design of a bivalent ligand, we were able to study ligand binding in the aptamer dimer at the molecular level. Spontaneous ligand-binding events, which are usually difficult to simulate, were observed and the contributing factors are described. These findings were further confirmed by in vivo experiments, where the cooperative binding effects of the bivalent ligands resulted in increased binding affinity compared to the native guanidinium ligand. Beyond ligand binding itself, the simulations revealed a novel, ligand-dependent base-stacking interaction outside of the binding pocket that stabilizes the riboswitch.

A global view of altered ligand-receptor interactions in bone marrow aging based on single-cell sequencing

Altered cell-cell communication is a hallmark of aging, but its impact on bone marrow aging remains poorly understood. Based on a common and effective pipeline and single-cell transcriptome sequencing, we detected 384,124 interactions including 2575 ligand-receptor pairs and 16 non-adherent bone marrow cell types in old and young mouse and identified a total of 5560 significantly different interactions, which were then verified by flow cytometry and quantitative real-time PCR. These differential ligand-receptor interactions exhibited enrichment for the senescence-associated secretory phenotypes. Further validation demonstrated supplementing specific extracellular ligands could modify the senescent signs of hematopoietic stem cells derived from old mouse. Our work provides an effective procedure to detect the ligand-receptor interactions based on single-cell sequencing, which contributes to understand mechanisms and provides a potential strategy for intervention of bone marrow aging.

Revealing molecular determinants governing mambalgin-3 pharmacology at acid-sensing ion channel 1 variants

Acid-sensing ion channels (ASICs) are trimeric proton-gated cation channels that play a role in neurotransmission and pain sensation. The snake venom-derived peptides, mambalgins, exhibit potent analgesic effects in rodents by inhibiting central ASIC1a and peripheral ASIC1b. Despite their distinct species- and subtype-dependent pharmacology, previous structure-function studies have focussed on the mambalgin interaction with ASIC1a. Currently, the specific channel residues responsible for this pharmacological profile, and the mambalgin pharmacophore at ASIC1b remain unknown. Here we identify non-conserved residues at the ASIC1 subunit interface that drive differences in the mambalgin pharmacology from rat ASIC1a to ASIC1b, some of which likely do not make peptide binding interactions. Additionally, an amino acid variation below the core binding site explains potency differences between rat and human ASIC1. Two regions within the palm domain, which contribute to subtype-dependent effects for mambalgins, play key roles in ASIC gating, consistent with subtype-specific differences in the peptides mechanism. Lastly, there is a shared primary mambalgin pharmacophore for ASIC1a and ASIC1b activity, with certain peripheral peptide residues showing variant-specific significance for potency. Through our broad mutagenesis studies across various species and subtype variants, we gain a more comprehensive understanding of the pharmacophore and the intricate molecular interactions that underlie ligand specificity. These insights pave the way for the development of more potent and targeted peptide analogues required to advance our understating of human ASIC1 function and its role in disease.

Transcriptional switches in melanoma T Cells: Facilitating polarizing into regulatory T cells

Melanoma is a malignant skin tumor with a high mortality rate. Regulatory T cells (Tregs) are immune cells with immunosuppressive roles, however, the precise mechanisms governing Treg involvement in melanoma remain enigmatic. Experimental findings unveiled different transcription factor switches between normal and tumor T cell, with heightened FOXP3 and BATF in the latter. These factors induced immunosuppressive molecules and Treg maintenance genes, polarizing tumor T cells into Tregs. Spatial transcriptomics illuminated the preferential settlement of Tregs at the melanoma periphery. Within this context, FOXP3 in Tregs facilitated direct enhancement of specific ligand gene expression, fostering communication with neighboring cells. Novel functional molecules bound to FOXP3 or BATF in Tregs, such as SPOCK2, SH2D2A, and ligand molecules ITGB2, LTA, CLEC2C, CLEC2D, were discovered, which had not been previously reported in melanoma Treg studies. Furthermore, we validated our findings in a large number of clinical samples and identified the Melanoma Treg-Specific Regulatory Tag Set (Mel TregS). ELISA analysis showed that the protein levels of Mel TregS in melanoma Tregs were higher than in normal Tregs. We then utilized SERS technology to measure the signal values of Mel TregS in exosome, and successfully discriminated between healthy individuals and melanoma patients, as well as early and late-stage patients. This approach significantly enhanced detection sensitivity. In sum, our research elucidated fresh insights into the mechanisms governing Treg self-maintenance and communication with surrounding cells in melanoma. We also introduced an innovative method for clinical disease monitoring through SERS technology.

NLRC5 senses NAD+ depletion, forming a PANoptosome and driving PANoptosis and inflammation

NLRs constitute a large, highly conserved family of cytosolic pattern recognition receptors that are central to health and disease, making them key therapeutic targets. NLRC5 is an enigmatic NLR with mutations associated with inflammatory and infectious diseases, but little is known about its function as an innate immune sensor and cell death regulator. Therefore, we screened for NLRC5's role in response to infections, PAMPs, DAMPs, and cytokines. We identified that NLRC5 acts as an innate immune sensor to drive inflammatory cell death, PANoptosis, in response to specific ligands, including PAMP/heme and heme/cytokine combinations. NLRC5 interacted with NLRP12 and PANoptosome components to form a cell death complex, suggesting an NLR network forms similar to those in plants. Mechanistically, TLR signaling and NAD+ levels regulated NLRC5 expression and ROS production to control cell death. Furthermore, NLRC5-deficient mice were protected in hemolytic and inflammatory models, suggesting that NLRC5 could be a potential therapeutic target.

Screening for promising multi-target bioactive components from Cortex Mori Radicis for the treatment of chronic cor pulmonale based on immobilized beta1-adrenergic receptor and beta2-adrenergic receptor chromatography

Cortex Morin Radicis (CMR) is the dried root bark of Morus alba. L. It has a variety of effects such as antibacterial, anti-tumour, treatment of cardiovascular diseases or upper respiratory tract disease and so on. The pursuit for drugs selected from Cortex Mori Radicis having improved therapeutic efficacy necessitates increasing research on new assays for screening bioactive compounds with multi-targets. In this work, we applied immobilized β1-AR and β2-AR as the stationary phase in chromatographic column to screen bioactive compounds from Cortex Morin Radicis. Specific ligands of the two receptors (e.g. esmolol, metoprolol, atenolol, salbutamol, methoxyphenamine, tulobuterol and clorprenaline) were utilized to characterize the specificity and bioactivity of the columns. We used high performance affinity chromatography coupled with ESI−MS to screen targeted compounds of Cortex Morin Radicis. By zonal elution, we identified morin as a bioactive compound simultaneously binding to β1-AR and β2-AR. The compound exhibited the association constants of 3.10 × 104 and 2.60 × 104 M−1 on the β1-AR and β2-AR column. On these sites, the dissociation rate constants were calculated to be 0.131 and 0.097 s−1. Molecular docking indicated that the binding of morin to the two receptors occurred on Asp200, Asp121, and Val122 of β1-AR, Asn312, Thr110, Asp113, Tyr316, Gly90, Phe193, Ile309, and Trp109 of β2-AR. Likewise, mulberroside C was identified as the bioactive compound binding to β2-AR. The association constants and dissociation rate constants were calculated to be 1.08 × 104 M−1 and 0.900 s−1. Molecular docking also indicated that mulberroside C could bind to β2-AR receptor on its agonist site. Taking together, we demonstrated that the chromatographic strategy to identify bioactive natural products based on the β1-AR and β2-AR immobilization, has potential for screening bioactive compounds with multi-targets from complex matrices including traditional Chinese medicines.

Surface-Bioengineered Extracellular Vesicles Seeking Molecular Biotargets in Lung Cancer Cells.

Personalized medicine is a new approach to modern oncology. Here, to facilitate the application of extracellular vesicles (EVs) derived from lung cancer cells as potent advanced therapy medicinal products in lung cancer, the EV membrane was functionalized with a specific ligand for targeting purposes. In this role, the most effective heptapeptide in binding to lung cancer cells (PTHTRWA) was used. The functionalization process of EV surface was performed through the C- or N-terminal end of the heptapeptide. To prove the activity of the EVs functionalized with PTHTRWA, both a model of lipid membrane mimicking normal and cancerous cell membranes as well as human adenocarcinomic alveolar basal epithelial cells (A549) and human normal bronchial epithelial cells (BEAS-2B) have been exposed to these bioconstructs. Magnetic resonance imaging (MRI) showed that the as-bioengineered PTHTRWA-EVs loaded with superparamagnetic iron oxide nanoparticle (SPIO) cargos reach the growing tumor when dosed intravenously in NUDE Balb/c mice bearing A549 cancer. Molecular dynamics (MD) in silico studies elucidated a high affinity of the synthesized peptide to the α5β1 integrin. Preclinical safety assays did not evidence any cytotoxic or genotoxic effects of the PTHTRWA-bioengineered EVs.

Structural perspectives on chemokine receptors.

Chemokine receptors are integral to the immune system and prime targets in drug discovery that have undergone extensive structural elucidation in recent years. We outline a timeline of these structural achievements, discuss the intracellular negative allosteric modulation of chemokine receptors, analyze the mechanisms of orthosteric receptor activation, and report on the emerging concept of biased signaling. Additionally, we highlight differences of G-protein binding among chemokine receptors. Intracellular allosteric modulators in chemokine receptors interact with a conserved motif within transmembrane helix 7 and helix 8 and exhibit a two-fold inactivation mechanism that can be harnessed for drug-discovery efforts. Chemokine recognition is a multi-step process traditionally explained by a two-site model within chemokine recognition site 1 (CRS1) and CRS2. Recent structural studies have extended our understanding of this complex mechanism with the identification of CRS1.5 and CRS3. CRS3 is implicated in determining ligand specificity and surrounds the chemokine by almost 180°. Within CRS3 we identified the extracellular loop 2 residue 45.51 as a key interaction mediator for chemokine binding. Y2917.43 on the other hand was shown in CCR1 to be a key determinant of signaling bias which, along with specific chemokine-dependent phosphorylation ensembles at the G-protein coupled receptors (GPCR's) C-terminus, seems to play a pivotal role in determining the direction of signal bias in GPCRs.

Assembly of Copper Alkynyl Clusters into Dimensionally Diverse Coordinated Polymers Mediated by Pyridine Ligands.

Surface ligands play crucial roles in modifying the properties of metal nanoclusters and stabilizing atomically precise structures, and also serve as vital linkers for constructing cluster-based coordination polymers. In this study, we present the results of the solvothermal synthesis of eight novel copper alkynyl clusters incorporating pyridine ligands using a one-pot method. The resulting compounds underwent characterization through elemental analysis, Fourier transform infrared (FT-IR) spectroscopy, powder X-ray diffraction (PXRD), and single-crystal X-ray diffraction (SCXRD). Our observations revealed that distinct pyridine ligands with varying lengths and coordination sites exert significant influence on the structure and dimensionality of the clusters. The structural diversity of these clusters led to the formation of one-dimensional (1D), two-dimensional (2D), or dimer arrangements linked by seven pyridine bridging ligands. Remarkably, these complexes exhibited unique UV-vis absorption and photoluminescence properties, which were influenced by the specific bridging ligand and structural framework. Furthermore, density functional theory (DFT) calculations demonstrated the capability of the conjugated system in the pyridine ligand to impact the band gap of clusters. This study not only unveils the inherent structural diversity in coordination polymers based on copper alkynyl clusters but also offers valuable insights into harnessing ligand engineering for structural and property modulation.

Screening and identification of DNA nucleic acid aptamers against F1 protein of Yersinia pestis using SELEX method.

Yersinia pestis is a bacterium that causes the disease plague. It has caused the deaths of many people throughout history. The bacterium possesses several virulence factors (pPla, pFra, and PYV). PFra plasmid encodes fraction 1 (F1) capsular antigen. F1 protein protects the bacterium against host immune cells through phagocytosis process. This protein is specific for Y. pestis. Many diagnostic techniques are based on molecular and serological detection and quantification of F1 protein in different food and clinical samples. Aptamers are small nucleic acid sequences that can act as specific ligands for many targets.This study, aimed to isolate the high-affinity ssDNA aptamers against F1 protein. In this study, SELEX was used as the main strategy in screening aptamers. Moreover, enzyme-linked aptamer sorbent assay (ELASA) and surface plasmon resonance (SPR) were used to determine the affinity and specificity of obtained aptamers to F1 protein. The analysis showed that among the obtained aptamers, the three aptamers of Yer 21, Yer 24, and Yer 25 were selected with a KD value of 1.344E-7, 2.004E-8, and 1.68E-8M, respectively. The limit of detection (LoD) was found to be 0.05, 0.076, and 0.033μg/ml for Yer 21, Yer 24, and Yer 25, respectively. This study demonstrated that the synthesized aptamers could serve as effective tools for detecting and analyzing the F1 protein, indicating their potential value in future diagnostic applications.

Advanced in Protein-Ligand Interaction Studies Optical-Based Spectroscopic Insights and Simulation Perspectives

Spectroscopic methods relying on light sources play a crucial role in the identification of protein-ligand interactions. Such experimental techniques open doors for scientists to employ them in disease prevention, treatment, drug synthesis, identification of pathways contributing to different disorders, and unveiling the chemical structure of receptors within the human body. Furthermore, alongside experimental approaches, simulation methods also find utility. The combination of both experimental and theoretical techniques enhances the robustness of researchers' investigations. Conversely, the human body harbors a myriad of distinct proteins, each possessing its own distinct structure and functionality; the disruption of any one of these may lead to a range of ailments. Proteins within the human body have the capacity to engage with diverse ligands, yielding intriguing outcomes. Not only proteins interact with other proteins, but they also engage with pharmaceuticals and other substances within the body. Examination of the bonding types formed between the protein and the specific ligand can be effectively accomplished through optical spectroscopic techniques and simulation inquiries. This paper provides a comprehensive review of recent optical spectroscopy methods, as well as simulation studies, which are currently being employed by researchers in these investigations.