Dissociation Constant Research Articles

Rapid Quantification of Oxytetracycline Based on Fluorescence Enhancement Influenced by pH.

Accurate quantification of antibiotics in environmental samples is typically challenging due to the low antibiotic concentrations and the complexity of environmental matrices. This paper presents a fluorescence spectrometry method for determining oxytetracycline under alkaline conditions. The ionic distribution of the oxytetracycline solution was analyzed based on its dissociation constant. The dimethylamino group plays a crucial role in this method, as it promotes intramolecular charge transfer in the electronic excited state through its electron-donating capability with a lone electron pair. The presented method is straightforward, cost-effective, and holds potential for analyzing oxytetracycline in water sample after further investigation.

Enhanced activation of signaling pathway by recombinant human adiponectin from genome-edited chickens

Adiponectin (ADPN) exerts various cellular and metabolic functions by activating signaling pathways, including extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) pathways, the protein kinase B (Akt) pathway, and the p38 mitogen-activated protein kinase (MAPK) pathway. However, generating functional recombinant human adiponectin (hADPN) in bacterial or mammalian cells is challenging. Although ADPN agonist peptides have been developed, problems like stability, solubility, and affinity for receptors remain. Recently, a genome-edited chicken bioreactor system was established, ensuring efficient ADPN production with optimal post-transcriptional modifications. We assessed the ability of egg white (EW)-derived hADPN, commercial hADPN, various ADPN agonist peptides, and globular ADPN on activation of the ERK1/2, Akt, and p38 MAPK pathways. EW-derived hADPN, abundant in hexamers and high molecular weight multimers, significantly phosphorylated ERK1/2 in serum-starved HEK293 cells after 15 min of treatment. Comparative analysis revealed that EW-derived hADPN and commercial hADPN induced greater phosphorylation of ERK1/2, Akt, and p38 MAPK than ADPN agonist peptides and globular ADPN, with EW-derived hADPN showing the highest activation. In summary, the finding that EW-derived hADPN strongly activates the ERK1/2, Akt, p38 MAPK signaling pathways highlights that an ADPN production system based on genome-edited chickens is an advantageous alternative to existing methods.

Inhibition of hERG K channels by verapamil at physiological temperature: Implications for the CiPA initiative

The Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative reassesses using the inhibition of hERG potassium channels by drugs as the major determinant for the potential to cause drug-induced Torsades de Pointes (TdP) cardiac arrhythmias. Here we report our findings on the next phase of CiPA: Determination of hERG inhibitory properties using the standard CiPA-defined data acquisition protocol, here called the standard protocol, at physiological temperature (37 degrees Celsius). To do this, we measured inhibition of hERG1a potassium channels stably expressed in HEK293 cells by the small molecule verapamil, using manual whole-cell patch-clamp electrophysiology recordings with the standard protocol, which is characterized, in part, by a series of 10 s duration voltage steps to 0 mV, ultimately leading to a cumulative recording time of approximately 30 min. Using the standard protocol, we measured an IC50 for verapamil of 225 nM, a Hill coefficient of 1, and time constant of inhibition at 0 mV of 0.64 s. But, using the standard protocol resulted in a very low (5 %) experimental success rate per cell, which had low practicality for future experiments. To address the 5 % success rate, we generated a revised protocol characterized, in part, by a series of 3 s duration voltage steps to 0 mV, leading to a cumulative recording time of approximately 10 min. Using the revised protocol, we found an IC50 for verapamil of 252 nM, a Hill coefficient of 0.8, and time constant of inhibition at 0 mV of 0.67 s. The values measured with the revised protocol were similar to those measured using the standard protocol and, furthermore, our success rate using the revised protocol rose to 25 %, an increase of 5-fold over the standard protocol, and more in line with the success rate for biophysical studies. In summary, we captured key pharmacological data for subsequent analysis in CiPA using a revised protocol with an increased success rate and an overall enhanced feasibility and practicality. We propose that the revised protocol may be more pragmatic for generation of some hERG channel drug inhibition data for CiPA and other regulatory sciences.

The Molecular and Biological Patterns Underlying Sustained SARS-CoV-2 Circulation in the Human Population

For four years, SARS-CoV-2, the etiological agent of COVID-19, has been circulating among humans. By the end of the second year, an absence of immunologically naive individuals was observed, attributable to extensive immunization efforts and natural viral exposure. This study focuses on delineating the molecular and biological patterns that facilitate the persistence of SARS-CoV-2, thereby informing predictions on the epidemiological trajectory of COVID-19 toward refining pandemic countermeasures. The aim of this study was to describe the molecular biological patterns identified that contribute to the persistence of the virus in the human population. For over three years since the beginning of the COVID-19 pandemic, molecular genetic monitoring of SARS-CoV-2 has been conducted, which included the collection of nasopharyngeal swabs from infected individuals, assessment of viral load, and subsequent whole-genome sequencing. We discerned dominant genetic lineages correlated with rising disease incidence. We scrutinized amino acid substitutions across SARS-CoV-2 proteins and quantified viral loads in swab samples from patients with emerging COVID-19 variants. Our findings suggest a model of viral persistence characterized by 1) periodic serotype shifts causing substantial diminutions in serum virus-neutralizing activity (> 10-fold), 2) serotype-specific accrual of point mutations in the receptor-binding domain (RBD) to modestly circumvent neutralizing antibodies and enhance receptor affinity, and 3) a gradually increasing amount of virus being shed in mucosal surfaces within a single serotype. This model aptly accounts for the dynamics of COVID-19 incidence in Moscow. For a comprehensive understanding of these dynamics, acquiring population-level data on immune tension and antibody neutralization relative to genetic lineage compositions is essential.

Inhibition of Key Virulence Enzymes of Botrytis cinerea by Flavonoids from the Antarctic Plant Colobanthus quitensis.

This study investigates the antifungal efficacy of flavonoids derived from Colobanthus quitensis against key virulence-related enzymes implicated in the pathogenic mechanisms of Botrytis cinerea. The flavonoids swertiajaponin, schaftoside, vitexin, and saponarin significantly inhibited pectinase, cellulase, and laccase activity. Specifically, swertiajaponin showed mixed inhibition of pectinase and cellulase, characterized by high affinity (low inhibition constant -Ki-) for enzyme-substrate complexes. Schaftoside showed mixed inhibition of pectinase and competitive inhibition of laccase, effectively reducing enzymatic activity by competing directly with the substrate. In contrast, vitexin showed competitive inhibition of pectinase and non-competitive inhibition of laccase, suggesting it induces conformational changes within the enzyme. Finally, saponarin uniquely showed uncompetitive inhibition of laccase, stabilizing the enzyme-substrate complex and thereby markedly reducing catalytic turnover. Supported by kinetic parameters (maximum velocity -Vmax-, Michaelis constant -Km-, and Ki), these findings highlight the potential of flavonoids from C. quitensis as natural fungicides, offering a sustainable and eco-friendly alternative to synthetic fungicides for managing agricultural diseases.

Protein-Sequence-Based Search of Nonreceptor ITAM-Like Regions to Identify Cytosolic Syk-Recruiting Proteins.

The recruitment of the protein spleen tyrosine kinase (Syk) to membrane-bound immune receptors is an essential step in initiating an immune response mediated through the activated receptors. Syk recognizes intracellular phosphorylated regions of membrane receptors known as immunoreceptor tyrosine-based activation motifs (ITAMs) defined by a sequence with two tyrosine (Y) amino acids separated by a certain spacing of six to eight residues: YXX(I/L)X6-8YXX(I/L). Syk with doubly phosphorylated ITAM is high-affinity and negatively regulated when Syk itself becomes phosphorylated. While the role of Syk in immune signaling is well characterized, recent information affords new functionality to Syk related to cytoplasmic processes, including the clearance of stress granules and P-bodies, both formed by liquid-liquid phase separation. Little to nothing is known about the molecular interactions involving Syk in these cytoplasmic processes. Given the essential role of receptor ITAMs in recruiting and localizing Syk for immune signaling, we explore here the possibility of a similar localization mechanism occurring for cytoplasmic processes by searching sequences of proteins related to Syk cytoplasmic function for regions that resemble receptor ITAMs. Protein sequence databases were generated from a Syk-dependent phosphoproteome and from genes related to P-bodies. A search of these databases for ITAM-like sequences yielded 102 unique hits, and 33 of these were synthesized and tested experimentally for binding to Syk tandem SH2 domains. The equilibrium dissociation constants were 0.1-50 μM for 28 peptides, and binding was negatively regulated by phosphorylation for many peptides. These results identify cytoplasmic proteins with potential for regulating the localization of Syk in a phosphorylation-dependent manner to nonmembrane cellular regions.

The dimerization domain of SARS CoV 2 Nucleocapsid protein is partially disordered as a monomer and forms a high affinity dynamic complex.

The SARS-CoV-2 Nucleocapsid (N) is a 419 amino acids protein that drives the compaction and packaging of the viral genome. This compaction is aided not only by protein-RNA interactions, but also by protein-protein interactions that contribute to increasing the valence of the nucleocapsid protein. Here, we focused on quantifying the mechanisms that control dimer formation. Single-molecule Förster Resonance Energy Transfer enabled us to investigate the conformations of the dimerization domain in the context of the full-length protein as well as the energetics associated with dimerization. Under monomeric conditions, we observed significantly expanded configurations of the dimerization domain (compared to the folded dimer structure), which are consistent with a dynamic conformational ensemble. The addition of unlabeled protein stabilizes a folded dimer configuration with a high mean transfer efficiency, in agreement with predictions based on known structures. Dimerization is characterized by a dissociation constant of ~ 12 nM at 23 °C and is driven by strong enthalpic interactions between the two protein subunits, which originate from the coupled folding and binding. Interestingly, the dimer structure retains some of the conformational heterogeneity of the monomeric units, and the addition of denaturant reveals that the dimer domain can significantly expand before being completely destabilized. Our findings suggest that the inherent flexibility of the monomer form is required to adopt the specific fold of the dimer domain, where the two subunits interlock with one another. We proposed that the retained flexibility of the dimer form may favor the capture and interactions with RNA, and that the temperature dependence of dimerization may explain some of the previous observations regarding the phase separation propensity of the N protein.

Experimental and theoretical vibrational analysis, structural conformations, DFT estimations, antibacterial, antifungal, DPPH,H2O2, Nitric oxide scavenging activity drug, in silico molecular docking, and ADMET studies of N-(2-carboxylphenyl) phthalimide (CPPD)

The title compound N-(2-carboxylphenyl) phthalimide (CPPD)was purchased with a stated purity of 99 % from M/S. Sigma-Aldrich Co. and utilized as such with no additional purification,CPPD is a thalidomide based derivative, which have led to the uses of most important drugs from 1950 and their mechanisms of action is essential for a better understanding of molecular targets with broad spectrum of biological activity. The obtained FTIR spectral data of the compound were compared to harmonic vibrational frequencies calculated using the ab initio DFT (B3LYP) technique with 6–311++G (d,p)basis sets. Furthermore, 13C and 1H NMR, first-order hyperpolarizability (βo) associated parameters (π, αo)of the compound, theSubsequent to recording the molecule’sUV–Visible spectra, DFT was used to analyze its electronic characteristics, including its HOMO and LUMO energies, molecular electrostatic potential (MESP), and Mulliken population studies were using ab initio DFT6-311++G (d,p)basis sets. Pharmacological Screening investigation of the title molecule showed a strong broad-spectrum of antifungal and antibacterial activity against various Gram (+) and Gram (−) bacteria using Ciprofloxacin as a positive control. The headline molecule is subjected toIn-silico molecular docking research with the purpose of improved recognize its biological activities, in addition with the minimal binding energy and hydrogen bond interaction that can view by Discovery Studio 4.0 visualizers. and drug likeness using Swiss ADME predictor (http://www.swissadme.ch/index.php) along with AdmetSAR-2.0 online software analysis tools features were investigated. The compound CPPD’s ability to degrade DPPH increased as a dose-dependent manner, with its maximal DPPH scavenging characteristic spanning from (18.2 ± 1.5 % to 73.2 ± 1.7 %) and maximum H2O2 scavenging trait ranging from (35.5 ± 5.3to 88.8 ± 3.1 %). The NO free radical scavenging property is linearly dependent on CPPD concentration. The interaction between the CPPD ligands and the 1HD2 protein is demonstrated by these data, as the protein displays a reduced binding energy value of −7.3 (Kcal/mol) and an inhibitory constant (ki) value of 4.39 μM. In swiss ADME prediction, CPPD is an evident from the physicochemical data that has an efficient receptor site binding mechanism. The lipophilicity of a drug is determined by its partition coefficient (Log P=log Po/w) between water and N-(2-carboxylphenyl) phthalimide. The paper further explains that the title compound can act as promising antibacterial and antioxidant agent throughin-vitro and molecular docking studies.

Brevetoxin Aptamer Selection and Biolayer Interferometry Biosensor Application.

Brevetoxins (PbTxs) are very potent marine neurotoxins that can cause an illness clinically described as neurologic shellfish poisoning (NSP). These toxins are cyclic polyether in chemistry and have increased their geographical distribution in the past 2 decades. However, the ethical problems as well as technical difficulties associated with currently employed analysis methods for marine toxins have spurred the quest for suitable alternatives to be applied in a regulatory monitoring regime. In this work, we reported the first instance of concurrent aptamer selection of Brevetoxin-1 (PbTx-1) and Brevetoxin-2 (PbTx-2) and constructed a biolayer interferometry (BLI) biosensor utilizing PbTx-1 aptamer as a specific recognition element. Through an in vitro selection process, we have, for the first time, successfully selected DNA aptamers with high affinity and specificity to PbTx-1 and PbTx-2 from a vast pool of random sequences. Among the selected aptamers, aptamer A5 exhibited the strongest binding affinity to PbTx-1, with an equilibrium dissociation constant (KD) of 2.56 μM. Subsequently, we optimized aptamer A5 by truncation to obtain the core sequence (A5-S3). Further refinement was achieved through mutations based on the predictions of a QGRS mapper, resulting in aptamer A5-S3G, which showed a significant increase in the KD value by approximately 100-fold. Utilizing aptamer A5-S3G, we fabricated a label-free, real-time optical BLI aptasensor for the detection of PbTx-1. This aptasensor displayed a broad detection range from 100 nM to 4000 nM PbTx-1, with a linear range between 100 nM and 2000 nM, and a limit of detection (LOD) as low as 4.5 nM. Importantly, the aptasensor showed no cross-reactivity to PbTx-2 or other marine toxins, indicating a high level of specificity for PbTx-1. Moreover, the aptasensor exhibited excellent reproducibility and stability when applied for the detection of PbTx-1 in spiked shellfish samples. We strongly believe that this innovative aptasensor offers a promising alternative to traditional immunological methods for the specific and reliable detection of PbTx-1.

Mechanisms of Cinnamomi Cortex against Diabetes Mellitus Explored by Network Pharmacology combined with Molecular Docking and Experimental Validation.

Cinnamomi cortex (CC), a traditional Chinese herbal medicine, exhibits antidiabetic properties, yet the underlying mechanisms are not fully understood. Our study combined network pharmacology, molecular docking, and experimental validation to elucidate the antidiabetic mechanisms of CC. Active components of CC and their potential antidiabetic targets were identified through TCMSP, DisGeNET, and GeneCards. The PPI networks were constructed with STRING and analyzed with Cytoscape, while GO and KEGG analyses utilized the DAVID database. Molecular docking with core targets was performed using Autodock Vina. The efficacy of CC in diabetes mellitus was evaluated through H&E staining, qPCR, and Western blot in the T2DM mouse. Eleven active components and sixty-six potential antidiabetic targets of CC were identified. The enrichment analysis revealed 288 GO terms and 37 pathways. The molecular docking showed high affinity for PPAR-γ and IL-6 receptors. In vivo studies further confirmed CC's ability to modulate PPAR-γ and IL-6, contributing to its antidiabetic effects. CC manages diabetes by regulating the PPAR-γ pathway and suppressing associated inflammation, providing a multi-pathway therapeutic approach.

Structural insight into the lead identification of a dual inhibitor of PDE1B and PDE10A: Integrating pharmacophore-based virtual screening, molecular docking, and structure-activity-relationship approaches

Schizophrenia is a chronic neuropsychiatric disorder affecting more than 1% of the world's population. Current antipsychotic treatments show inadequacy in mitigating the negative and cognitive symptoms of schizophrenia. In addition, these medications cause undesirable extrapyramidal side effects. According to the studies, inhibition of phosphodiesterase (PDE) 1B and PDE10A simultaneously can alleviate positive, negative, and cognitive symptoms of schizophrenia. Thus, this study aims to identify new dual inhibitors of PDE1B and PDE10A using ligand-based pharmacophore modelling, virtual screening, and molecular docking studies. Accordingly, the generated pharmacophore models of PDE1B and PDE10A comprised hydrogen bond acceptor, aromatic ring, and hydrophobic features. These features were essential for retrieving the active hits from the Universal Natural Product Database in the virtual screening. Additional filters were subsequently employed to identify potential hits that could be developed into central nervous system-active compounds. Hits meeting all the screening criteria were subjected to docking studies with PDE1B and PDE10A. Among these hits, UNPD167314 exhibited significant binding affinities for the target receptors. It occupied the P-clamp and displayed hydrophobic, aromatic, and hydrogen bond interactions with the active site residues of both receptors, thus selected as a lead compound for the design of potent and selective dual inhibitors. The structural modifications of UNPD167314 resulted in the design of 35 novel inhibitors. Out of 35, four compounds exhibited high and comparable binding affinities for both PDE1B and PDE10A, making them promising candidates for further evaluation and optimisation.

Anti-inflammatory potential of polyphenols: Combining in silico prediction and in vivo data

Introduction: Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by joint inflammation and destruction, leading to significant pain and disability. Adenosine deaminase (ADA) is identified as a biomarker for RA’s inflammatory process. This study aims to investigate the potential of flavonoids and phenolic acids to inhibit ADA activity (in silico) and evaluate their anti-inflammatory effects in a RA model (in vivo). Methods: The molecular docking study was conducted using YASARA Structure 19.12.14. software following the Auto Dock 4.2 protocol. A rat model with pristane-induced arthritis was used to test the anti-inflammatory effect of selected polyphenols. The consistency of the development of the rat model was evaluated through the following indicators artistic score, paw volume, and body weight. Quercetin was administered intragastrically at doses of 150 and 400 mg/kg over 15 days. The C-reactive protein (CRP) level in serum was measured with an automatic biochemical analyzer. Statistical analyses were performed using SPSS 29.0.2.0. Results: Molecular docking simulations showed flavonoids inhibited ADA activity with inhibition constants ranging from 0.012 mM to 0.190 mM. In the in vivo RA model, quercetin significantly reduced joint inflammation and serum CRP levels at a higher dose of 400 mg/kg. Conclusion: Quercetin shows promise as an anti-inflammatory agent for RA by targeting ADA, suggesting that flavonoid-rich plant extracts could enhance RA treatment.

Using a dual immunoinformatics and bioinformatics approach to design a novel and effective multi-epitope vaccine against human torovirus disease

Human Torovirus (HToV), a member of the Coronaviridae family, causes severe enteric diseases with no specific medication available. To develop novel preventative measures, we employed immunoinformatics techniques to design a multi-epitope-based subunit vaccine (HToV-MEV) triggering diverse immune responses. We selected non-allergenic, non-toxic, and antigenic epitopes from structural polyproteins, joined them with suitable linkers, and added an adjuvant 50S ribosomal L7/L12 peptide. The vaccine's solubility score of 0.903678 and physiochemical properties were found effective. Molecular dynamics simulations and free energy calculations revealed strong binding affinity for Toll-like receptor 3 (TLR-3), with a lowest energy score of −303.88, indicating high affinity. In-silico cloning and codon optimization showed significant production potential in E. coli. Immune simulations predicted a human immunological response. Our results are promising, but subsequent in vivo research is recommended. The HToV-MEV vaccine design demonstrates potential for preventing HToV-related diseases, and further investigation is warranted to explore its therapeutic applications.

Transglutaminase–mucin binding dynamics in gastrointestinal mucus: Interfacial behaviour, thermodynamics and gelation mechanism

Transglutaminase, an enzyme present in epithelial cells and as a residual component in processed foods, is hypothesised to interact with gastrointestinal mucus, impacting its structure and function. To test the physical validity of this phenomenon, this study investigates the binding kinetics and thermodynamics between porcine gastric mucin (PGM) and microbial transglumatinse (TGM) in a model gastrointestinal mucus, followed by the rheological analysis of the resulting systems. At pH 7, TGM exhibited pronounced binding with the PGM interface, characterised by a high surface density (55.34 ± 1.86 µg/m−2) and a low dissociation constant (KD ∼ 4.03 ± 0.10 μM) as determined by surface plasma resonance (SPR). Conversely, at pH 3, TGM showed weak adhesion onto PGM, resulting in a less stable binding, reflected by a lower surface density (10.94 ± 0.67 µg/m−2) and a higher dissociation constant (KD ∼ 6.24 ± 0.22 μM). Regardless of the nature of interaction, the Hill coefficients (nH ≥ 1) indicated that the binding sites were markedly denser at pH 7 (1383.38 ± 46.47 pmol/m−2), than at pH 3 (273.68 ± 16.84 pmol/m−2). Fluorimetry analysis suggested temperature-dependent dynamic binding between PGM and TGM. The resulting Benesi – Hildebrand plots illustrated a linear correlation between PGM and increasing TGM concentration, suggesting a single-step interaction mechanism. The calculated thermodynamic parameters indicated spontaneous interaction between PGM and TGM (ΔG < 0) via endothermic (entropic) interactions (ΔH > 0). Notably, hydrophobic forces played a significant role in the network stabilisation of PGM−TGM complex (ΔS > 0). Rheometry analysis elucidates that the interaction maxima within TGM−PGM systems substantially elevate both shear viscosity (η), and the melting point (Tm), shifting from 6.75 ± 0.28 to 70.94 ± 2.21 (×10−3) Pa s (at 1 s−1), and 36.80 ± 0.80 to 48.20 ± 0.11 °C, respectively. Furthermore, the coexistence of these two macromolecular species results in a 3- to 4-fold dramatic increase in the viscoelastic moduli of the binary complex. These findings build a strong physicochemical basis for the interaction between TGM and PGM, with profound effects on the rhological behaviour of the latter; it also highlights the need to examine the biochemical/enzymatic aspects of said interactions, and their potential effects on mucosa and human physiology.

Abstract A070: Time-Dependent Oxidation and Aggregation of Vimentin upon Binding by β-lap Induced Immunogenic Cell Death

Abstract β-lapachone (β-lap) has been demonstrated as an NAD(P)H:quinone oxidoreductase1 (NQO1) bioactivatable compound. It initiated a futile redox cycle catalyzed by NQO1, resulting in reactive oxygen species (ROS) generation, with consumption of the reductive NAD(P)H. After a 4-h pulse of sufficiently lethal dose of β-lap, high levels of ROS diffused into nuclei to induce tumor-selective DNA damage and programmed necrosis in cancers overexpressing NQO1. Recently, our experiments showed that prolonged low dose β-lap administration exerted significant and NQO1 independent antitumor efficacy in mouse models with no overt signs of toxicity. Thus, we synthesized a photoactive β-lap probe to identify the molecular target of β-lap. Vimentin, a major constituent of the intermediate filament family of proteins, was identified as the direct binding target of β-lap. Vimentin was highly upregulated in multiple cancers including PDAC, and was a binding partner of β-lap with a dissociation constant at micromolar levels. Ligand binding assays in Panc1 cells employing β-lap as a specific competitor showed that vimentin was bound by β-lap-probe in a β-lap-competitive manner, and further confirmed that the in vivobinding target of β-lap was vimentin. Moreover, it was manifested that endogenous vimentin mRNA levels directly correlated with sensitivity to prolonged exposure of β-lap in a panel of pancreatic cancer cell lines, and knockout of vimentin in Panc1 cells markedly decreased lethality after prolonged exposure of β-lap. Mechanistically, we revealed that β-lap bound to vimentin and induced disulfide bonds that participated in disulfide cross-linking between a pair of vimentin dimers in a concentration and time dependent manner, forming vimentin oligomers of approximately 150 kDa. Prolonged exposure of β-lap promoted the disruption of filament architecture and vimentin degradation, ultimately resulting in cell death. In addition, the cell death by targeting vimentin exhibited a more inflammatory condition and enhanced DC activation. Together, our findings unveiled an unknown molecular target for β-lap and provided valuable insights into its mechanism of action. Targeting vimentin also presented a new strategy that inhibited the tumor growth and synergized with immunotherapy to disrupt immune evasion and reduce immune suppression against pancreatic cancers. Citation Format: Feng Qian, Lei Dou, Kaixin Wang, Yi Xia, Zhidong Chen, Yumeng Zu, Shuang Xi. Time-Dependent Oxidation and Aggregation of Vimentin upon Binding by β-lap Induced Immunogenic Cell Death [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A070.

Stabilization of dimeric PYR/PYL/RCAR family members relieves abscisic acid-induced inhibition of seed germination

Abscisic acid (ABA) is the primary preventing factor of seed germination, which is crucial to plant survival and propagation. ABA-induced seed germination inhibition is mainly mediated by the dimeric PYR/PYL/RCAR (PYLs) family members. However, little is known about the relevance between dimeric stability of PYLs and seed germination. Here, we reveal that stabilization of PYL dimer can relieve ABA-induced inhibition of seed germination using chemical genetic approaches. Di-nitrobensulfamide (DBSA), a computationally designed chemical probe, yields around ten-fold improvement in receptor affinity relative to ABA. DBSA reverses ABA-induced inhibition of seed germination mainly through dimeric receptors and recovers the expression of ABA-responsive genes. DBSA maintains PYR1 in dimeric state during protein oligomeric state experiment. X-ray crystallography shows that DBSA targets a pocket in PYL dimer interface and may stabilize PYL dimer by forming hydrogen networks. Our results illustrate the potential of PYL dimer stabilization in preventing ABA-induced seed germination inhibition.

Identification of the Potential Role of the E4orf4 Protein in Adenovirus A, B, C, and D Groups in Cancer Therapy: Computational Approaches.

The human adenovirus (HADV) early region 4 open reading frame 4 (E4orf4) protein plays a regulatory role in promoting viral infection by interacting with various cellular proteins. E4orf4 can induce death in cancer cells. One of the death pathways that is induced by this protein is related to the formation of membrane blebbing following the phosphorylation of tyrosine amino acids. The activation of this pathway requires the interaction of E4orf4 with Src family kinases (SFKs). The modulation mechanism of Src-dependent signaling via E4orf4 is not yet fully understood. However, evidence suggests that a physical association between the Src kinase domain and the arginine-rich motif of E4orf4 is crucial. Physically connecting E4orf4 to Src kinase leads to the deregulation of the Src-related signaling pathway, thereby inducing cytoplasmic death. In this study, we mapped the E4orf4 interaction site in Src to investigate the interaction between E4orf4 and Src in detail. We also compared the binding strength of E4orf4 proteins from different HADV groups. To this end, we performed bioinformatics structural analysis of the Src kinase domain and E4orf4 to identify E4orf4 interaction sites. The group with the lowest binding energy was predicted to be the most likely candidate for the highest cytoplasmic death in tumor cells based on the energy of the E4orf4-Src complex in various HADV groups. These results show that HADV-A and HADV-C have minimal binding energies to the E4orf4-Src complex, while the dissociation constant (Kd) of HADV-A was less than that of HADV-C. According to the obtained results, E4orf4 of the HADV-A group is more effective at triggering cytoplasmic death based on its most robust interaction with the Src kinase domain.

1-MCP Triggering Coffee Anthesis and Its Effects on Binding Affinity and Gene Expression of Different Ethylene Receptors

1-MCP Triggering Coffee Anthesis and Its Effects on Binding Affinity and Gene Expression of Different Ethylene Receptors

Dissociation role on the catalytic activity of organic halides in CO2 conversion to cyclic carbonates: Experimental and computational study

There is a limited number of systematic CO2 conversion studies that provide a clear understanding of the effect of the active sites of catalysts. Hence, this work examines the catalytic activity of 24 organic salts consisting of chloride, bromide or iodide anions and imidazolium, ammonium, or phosphonium-based cations, in the synthesis of hexylene and styrene carbonates from CO2, resulting in a diverse range of yields. The findings revealed that high yields depend heavily on catalyst solubility in the reaction medium, but solubility alone does not guarantee reaction success. This finding supports the new hypothesis that catalyst dissociation, reliant on solubility, is a critical factor in defining the catalytic activity. A strong correlation was observed between carbonate yields and the dissociation constants of catalysts, calculated using the COSMO-RS method. This suggests that greater dissociation, reflecting weaker cation-anion interactions, facilitates the anion nucleophilic attack on the epoxide. Also, the relationship between calculated dissociation constant and experimental ionic conductivity was successfully validated. This highlights the significance of organic salt dissociation on catalytic performance and validates the use of computational tools to predict key operational parameters, enhancing the understanding and optimization of CO2 conversion into cyclic carbonates.

Discovery of Novel Neo-Clerodane Derivatives as Potent Dual-Functional Antiosteoporosis Agents through Targeting Peroxisome Proliferator-Activated Receptor-γ.

A library of 31 natural neo-clerodanes isolated from Ajuga decumbens was assayed for antiosteoporosis. This results in 18 neo-clerodane osteoclastogenesis inhibitors, and compound 3 prevents bone loss in vivo. Further mechanistic studies demonstrated that these compounds inhibit osteoporosis by antagonizing peroxisome proliferator-activated receptor-γ (PPARγ). We designed and synthesized 17 compounds by chemically modifying the natural neo-clerodane 19 (highly potent and the major composition of A. decumbens extract) by means of structure-based drug design techniques. Among these neo-clerodane derivatives, compound 34 is the most potent osteoporosis inhibitor with a 46-fold improvement in inhibiting osteoclastogenesis (IC50 = 0.042 vs 1.92 μM), 11-fold increased activity in PPARγ antagonism (EC50 = 0.75 vs 8.35 μM), 66-fold enhancement in receptor affinity (KD = 0.27 vs 17.7 μM), and enhanced osteogenic promotion compared to 19. This underscores the potential of neo-clerodane diterpenoids as promising leads for osteoporosis treatment by targeting PPARγ.