High Affinity Binding Research Articles

Computational Design of a Novel Inhibitor Against COVID

Background: In recent years, in silico computational approaches have tremendously guided computational medicinal chemists and research scientists to analyze protein structures, kinetics, functions, and molecular interactions of the administered drugs. Objective: This study aimed to identify a novel inhibitor against SARS-CoV-2 using human CD26 and modeled spike protein through suitable in silico approaches. Methods: In this work, molecular docking and molecular dynamics simulation experiments were conducted to gain insights into the binding affinity and stability, respectively. The docked complex of CD26 with modeled spike protein showed higher binding affinity than the complex of CD26 with resolved spike protein due to the existence of strong interactions with the crucial amino acid residues of the target proteins. Results: The results of the molecular dynamics simulation demonstrated that CD26 with the modeled spike protein docked complex showed good stability when compared with the resolved protein. Conclusion: From this computational finding, it was also suggested that the structure was stable and would rapidly guide the discovery of potential inhibitors against COVID-19.

In-silico based Designing of benzo[d]thiazol-2-amine Derivatives as Anal-gesic and Anti-inflammatory Agents.

Benzo[d]thiazoles represent a significant class of heterocyclic com-pounds renowned for their diverse pharmacological activities, including analgesic and anti-inflammatory properties. This molecular scaffold holds substantial interest among medicinal chemists owing to its structural versatility and therapeutic potential. Incorporating the benzo[d]thiazole moiety into drug molecules has been extensively investigated as a strategy to craft novel therapeutics with heightened efficacy and minimized adverse effects. The aim of the present research work was to design, synthesize and characterize the new benzo[d]thiazol-2-amine derivatives as potent analgesic and anti-inflammatory agents. The synthesis of the presented benzo[d]thiazol-2-amine derivatives was performed by condensing-(4-chlorobenzylidene) benzo[d]thiazol-2-amine with a number of substituted phenols in the presence of potassium iodide and anhydrous potassium carbonate in dry acetone. IR spectroscopy, 1HNMR spectroscopy, 13CNMR spectroscopy and Mass spectroscopy methods were used to characterize the structural properties of all 13 newly syn-thesized derivatives. The molecular properties of these newly synthesized derivatives were estimated to study the attributes of drug-like candidates. Benzo[d]thiazol-2-amine derivatives were molecularly docked with selective enzymes COX-1 and COX-2. Analgesic and anti-inflammatory activities of synthesized compounds were evaluated by us-ing albino rats. Findings of the research suggested that compounds G3, G4, G6, G8 and G11 possess higher binding affinity than diclofenac sodium, when docking was performed with enzyme COX-1. Compounds G1, G3, G6, G8andG10 showed lower binding affinity than Indometha-cin when docking was performed with enzyme COX-2.In vitro evaluation of the COX-1 and COX-2 enzyme inhibitory activities was performed for synthesized compounds. Compounds G10 and G11 exhibited significant COX-1 and COX-2 enzyme in-hibitory action with an IC50 value of 5.0 and 10 μM, respectively. Using the hot plate method and the carrageenan-induced rat paw edema model, the synthesized compounds were screened for their biological activities, including analgesic and anti-inflammatory activities. Highest analgesic action was exhibited by derivative G11 and the compound G10 showed the highest anti-inflammatory response. Inhibition of COX may be considered as a mechanism of action of these compounds. It was concluded that synthesized derivatives G10 and G11 exhibited significant analgesic and anti-inflammatory effect; therefore, the said compounds may be subjected to further clinical investigation for establishing these as future compounds for the treatment of pain and inflammation.

Targeting PERK and GRP78 in colorectal cancer: Genetic insights and novel therapeutic approaches

Colorectal cancer (CRC) ranks among the leading causes of cancer-related deaths worldwide. Enhancing CRC diagnosis and prognosis requires the development of improved biomarkers and therapeutic targets. Emerging evidence suggests that the unfolded protein response (UPR) plays a pivotal role in CRC progression, presenting new opportunities for diagnosis, treatment, and prevention. This study hypothesizes that genetic variants in endoplasmic reticulum (ER) stress response genes influence CRC susceptibility. We examined the frequencies of SNPs in PERK (rs13045) and GRP78/BiP (rs430397) within a South Iranian cohort.We mapped the cellular and molecular features of PERK and GRP78 genes in colorectal cancer, observing their differential expressions in tumor and metastatic tissues. We constructed co-expression and protein-protein interaction networks and performed gene set enrichment analysis, highlighting autophagy as a significant pathway through KEGG. Furthermore, the study included 64 CRC patients and 60 control subjects. DNA extraction and genotyping were conducted using high-resolution melting (HRM) analysis. Significant differences in PERK and GRP78 expressions were observed between CRC tissues and controls. Variations in PERK and GRP78 genotypes were significantly correlated with CRC risk. Utilizing a Multi-Target Directed Ligands approach, a dual PERK/GRP78 inhibitor was designed and subjected to molecular modeling studies. Docking experiments indicated high-affinity binding between the proposed inhibitor and both genes, PERK and GRP78, suggesting a novel therapy for CRC.These findings highlight the importance of understanding genetic backgrounds in different populations to assess CRC risk. Polymorphisms in UPR signaling pathway elements may serve as potential markers for predicting CRC susceptibility, paving the way for personalized therapeutic strategies.

De Novo Rational Design of Peptide-Based Protein-Protein Inhibitors (Pep-PPIs) Approach by Mapping the Interaction Motifs of the PP Interface and Physicochemical Filtration: A Case on p25-Cdk5-Mediated Neurodegenerative Diseases.

Protein-protein interactions, or PPIs, are a part of every biological activity and have been linked to a number of diseases, including cancer, infectious diseases, and neurological disorders. As such, targeting PPIs is considered a strategic and vital approach in the development of new medications. Nonetheless, the wide and flat contact interface makes it difficult to find small-molecule PP inhibitors. An alternative strategy would be to use the PPI interaction motifs as building blocks for the design of peptide-based inhibitors. Herein, we designed 12-mer peptide inhibitors to target p25-inducing-cyclin-dependent kinase (Cdk5) hyperregulation, a PPI that has been shown to perpetuate neuroinflammation, which is one of the major causal implications of neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and frontotemporal dementia. We generated a library of 5 062 500 peptide combination sequences (PCS) derived from the interaction motif of Cdk5/p25 PP interface. The 20 amino acids were differentiated into six groups, namely, hydrophobic (aliphatic), aromatic, basic, acidic, unique, and polar uncharged, on the basis of their physiochemical properties. To preserve the interaction motif necessary for ideal binding, de novo modeling of all possible peptide sequence substitutions was considered. A set of filters, backed by the Support Vector Machine (SVM) algorithm, was then used to create a shortlisted custom peptide library that met specific bioavailability, toxicity, and therapeutic relevance, leading to a refined library of 15 PCS. A greedy algorithm and coarse-grained force field were used to predict peptide structure and folding before subsequent modeling studies. Molecular docking was performed to estimate the relative binding affinities, and out of the top hits, Pep15 was subjected to molecular dynamics simulations and binding free-energy calculations in comparison to a known peptide inhibitor with experimental data (template peptide). Interestingly, the identified peptide through our protocol, Pep15, was found to show a significantly higher binding affinity than the reference template peptide (-48.10 ± 0.23 kcal/moland -17.53 ± 0.27 kcal/mol, respectively). In comparison to the template peptide, Pep15 was found to possess a more compact and buried surface area, tighter binding landscape, and reduced conformational variability, leading to enhanced structural and kinetic stability of the Cdk5/p25 complex. Notably, both peptide inhibitors were found to have a minimal impact on the architectural integrity of the Cdk5/p25 secondary structure. Herein, we propose Pep15 as a novel and potentially disruptive peptide drug for Cdk5/p25-mediated neurodegenerative phenotypes that require further clinical investigation. The systematic protocol and findings of this report would serve as a valuable tool in the identification of critical PPI interface reactive residues, designing of analogs, and identification of more potent peptide-based PPI inhibitors.

The potency of <i>Elaeocarpus grandiflorus </i>Leaf Extract as Anti-obesity: <i>in vivo </i>and <i>in silico</i> Study

The research aims to determine the effect of ethanol extract of Elaeocarpus grandiflorus leaves extract as anti-obesity by in vivo and silico computational models. The pre-and -post-tests were carried out on 20 female Wistar rats, divided into 4 groups. The control group (K) received no treatment and the experimental groups were treated with E. grandiflorus extract of 200 mg/kg BW (P1), 400 mg/kg BW (P2), and 800 mg/kg BW (P3) for 14 days. The body weight, abdominal circumference, and abdominal fat mass were measured on Day 1 and Day 15. The results showed differences in body weight (p=0.02), abdominal circumference (p=0.01), and abdominal fat mass (p=0.00). In silico exploration, bioactive compounds of rutin, orientin, luteolin, vitexin, iso orientin, isovitexin, kaempferol, and quercetin were identified, and targeted ELAVL1, IGF1R, CREB1, AKT1, and PIK3R1 of the AMPK signaling pathway that involved in the anti-obesity mechanism. The high binding affinity values was rutin-EVAL1 (-9.3), orientin-ELAVL1 (-8.3), and quercetin- IGFR1 (-8.2). It can be concluded that the ethanol extract of E. grandiflorus leaves has the potential to be developed as an anti-obesity agent.

Antimicrobial potentials of Pandanus amaryllifolius Roxb.: Phytochemical profiling, antioxidant, and molecular docking studies.

The emergence of antimicrobial resistance has led to an urgent need for novel antimicrobial drugs. This study aimed to determine the antioxidant and antimicrobial potentials in silico and in vitro of Pandanus amaryllifolius Roxb. ethanolic extract. The extracts were subjected to gas chromatography-mass spectrometry (GC-MS) analysis to identify the compounds. In silico antimicrobial studies were performed to gain insights into the possible mechanism of action of the active compounds as antimicrobials. The antimicrobial activities of the ethanolic extracts were assessed using the agar well diffusion method against the Surabaya strain of Escherichia coli and Staphylococcus aureus. Antioxidant properties of the extract were done using DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) and ABTS [2,2'-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid)] inhibition assays. The phytochemical screening revealed that the extract has high flavonoids and polyphenols contents. The GC-MS analysis detected the presence of 52 bioactive substances, with n-hexadecanoic acid, 9, 12, 15-octadecatrienoic acid, benzofuran 2,3-dihydro-. quinic acid, neophytadiene as major compound. Molecular docking studies showed that these compounds have a high binding affinity towards the target proteins, thereby inhibiting their activities. The ethanolic extract of P. amaryllifolius Roxb. exhibited antioxidant and antimicrobial activities. The IC50 were 11.96 ± 4.01 μg/ml and 26.18 ± 7.44 μg/ml for DPPH and ABTS. The diameters of inhibition zones (DIZ) and percentage of inhibition (PI) were calculated and varied for every single pathogen 16.44 ± 1.21mm/66.76 ± 4.92% (50%) and 21.22 ± 0.11mm/82.49 ± 3.91% (50%) for E. coli and S. aureus (DIZ/PI) respectively. Overall, this study provides information on the mechanism responsible for P. amaryllifolius Roxb. extract as a natural antimicrobe and lays the foundation for further studies to isolate and characterize the active compounds as antimicrobial candidates.

Nonequilibrium Antigen Recognition during Infections and Vaccinations

The initial immune response to an acute primary infection is a coupled process of antigen proliferation, molecular recognition by naive B cells, and their subsequent clonal expansion. This process contains a fundamental problem: the recognition of an exponentially time-dependent antigen signal. Here, we show that an efficient immune response must be stringently constrained to B-cell lineages with high antigen binding affinity. We propose a tuned proofreading mechanism for primary recognition of new antigens, where the molecular recognition machinery is adapted to the complexity of the immune repertoire. We show that this process produces potent, specific, and fast recognition of antigens, maintaining a spectrum of genetically distinct B-cell lineages as input for affinity maturation. Our analysis maps the proliferation-recognition dynamics of a primary infection to a generalized Luria-Delbrück process, akin to the dynamics of the classic fluctuation experiment. This map establishes a link between signal recognition dynamics and evolution. We derive the resulting statistics of the activated immune repertoire: Antigen binding affinity, expected size, and frequency of active B-cell clones are related by power laws, which define the class of generalized Luria-Delbrück processes. Their exponents depend on the antigen and B-cell proliferation rate, the number of proofreading steps, and the lineage density of the naive repertoire. We extend the model to include spatiotemporal processes, including the diffusion-recognition dynamics of a vaccination. Empirical data of activated mouse immune repertoires are found to be consistent with activation involving about three proofreading steps. The model predicts key clinical characteristics of acute infections and vaccinations, including the emergence of elite neutralizers and the effects of immune aging. More broadly, our results establish infections and vaccinations as a new probe into the global architecture and functional principles of immune repertoires. Published by the American Physical Society 2024

Expression of Growth Hormone-Releasing Hormone and Its Receptor Splice Variants in a Cohort of Hungarian Pediatric Patients with Hematological and Oncological Disorders: A Pilot Study.

Hematological and oncological diseases are still among the leading causes of childhood mortality. Expression of growth hormone-releasing hormone (GHRH) and its receptors (GHRH-R) has been previously demonstrated in various human tumors, but very limited findings are available about the presence and potential function of GHRH-Rs in oncological and hematological disorders of children. In this study, we aimed to investigate the expression of mRNA for GHRH and splice variant 1 (SV) of GHRH-R in 15 pediatric hematological/oncological specimens by RT-PCR. The presence and binding characteristics of GHRH-R protein were also studied by Western blot and ligand competition assays. Of the fifteen specimens studied, eleven pediatric samples (73%) showed the expression of mRNA for GHRH. These eleven samples also expressed mRNA for GHRH receptor SV1. GHRH-R protein was found to be expressed in two benign tumor samples and five malignant tumors examined by Western blot. The presence of specific, high affinity binding sites on GHRH-R was demonstrated in all of the seven human pediatric solid tumor samples investigated. Our results show that the expression of GHRH and SV1 of GHRH-R in hemato-oncological diseases in children can pave the way for further investigation of GHRH-Rs as potential molecular targets for diagnosis and therapy.

Computational drug repositioning for IL6 triggered JAK3 in rheumatoid arthritis using FDA database.

Rheumatoid Arthritis (RA) is a persistent autoimmune disease affecting approximately 0.5-1 percent of the world population. RA prevalence is higher in woman aged between 35 and 50years than in age matched men, though this difference is less evident among elderly patients. The profound immune specific effects of disrupted JAK 3 (Janus kinase 3) signaling highlight the possibility of therapeutic targeting of JAK3 as a highly specific mode of immune system suppression. To address the above problem which is unendurable to patients and in the hope to cater some respite to such suffering we have targeted JAK 3 protein and JAK/STAT signaling pathway with compounds downloaded from FDA database, and performed screening of all available compounds docked against JAK3 protein. The difference between the target protein and other proteins of the same family was studied using cross docking and the compounds having higher binding affinity to JAK3 protein also showed more selectivity towards the particular protein. Density functional theory and molecular dynamics simulation study was done to study the compounds at their atomic level to know more about their drug likeliness. At the end of the study and based on our analysis we have come up with three FDA approved drugs that can be proposed as a treatment option for Rheumatoid Arthritis.

Single Chelator-Minibody Theranostic Agents for 89Zr PET Imaging and 177Lu Radiopharmaceutical Therapy of PSMA-Expressing Prostate Cancer.

Here we describe an anti-prostate-specific membrane antigen (PSMA) minibody (IAB2MA) conjugated to an octadentate, macrocyclic chelator based on four 1-hydroxypyridin-2-one coordinating units (Lumi804 [L804]) labeled with 89Zr (PET imaging) and 177Lu (radiopharmaceutical therapy), with the goal of developing safer and more efficacious treatment options for prostate cancer. Methods: L804 was compared with the current gold standard chelators, DOTA and deferoxamine (DFO), conjugated to IAB2MA for radiolabeling with 177Lu and 89Zr in cell binding, preclinical biodistribution, imaging, dosimetry, and efficacy studies in the PSMA-positive PC3-PIP tumor-bearing mouse model of prostate cancer. Results: Quantitative radiolabeling (>99% radiochemical yield) of L804-IAB2MA with 177Lu or 89Zr was achieved at ambient temperature in under 30 min, comparable to 89Zr labeling of DFO-IAB2MA. In contrast, DOTA-IAB2MA was radiolabeled with 177Lu for 30 min at 37°C in approximately 90% radiochemical yield, requiring further purification. Using europium(III) as a luminescent surrogate, high binding affinity of Eu-L804-IAB2MA to PSMA was demonstrated in PC3-PIP cells (dissociation constant, 4.6 ± 0.6 nM). All 4 radiolabeled constructs showed significantly higher levels of internalization after 30 min in the PC3-PIP cells than in PSMA-negative PC3-FLU cells. The accumulation of 177Lu- and 89Zr-L804-IAB2MA in PC3-PIP tumors and all organs examined (i.e., heart, liver, spleen, kidney, muscle, salivary glands, lacrimal glands, carcass, and bone) was significantly lower than that of 177Lu-DOTA-IAB2MA and 89Zr-DFO-IAB2MA at 96 and 72 h after injection, respectively. Generally, SPECT/CT and PET/CT imaging data showed no significant difference in the SUVmean of the tumors or muscle between the radiotracers. Dosimetry analysis via both organ-level and voxel-level dose calculation methods indicated significantly higher absorbed doses of 177Lu-DOTA-IAB2MA in tumors, kidney, liver, muscle, and spleen than of 177Lu-L804-IAB2MA. PC3-PIP tumor-bearing mice treated with single doses of 177Lu-L804-IAB2MA (18.4 or 22.2 MBq) exhibited significantly prolonged survival and reduced tumor volume compared with unlabeled minibody control. No significant difference in survival was observed between groups of mice treated with 177Lu-L804-IAB2MA or 177Lu-DOTA-IAB2MA (18.4 or 22.2 MBq). Treatment with 177Lu-L804-IAB2MA resulted in lower absorbed doses in tumors and less toxicity than that of 177Lu-DOTA-IAB2MA. Conclusion: 89Zr- and 177Lu-L804-IAB2MA may be a promising theranostic pair for imaging and therapy of prostate cancer.

1, 6-dilauroyl-D-fructofuranose ameliorates lipopolysaccharide induced sepsis acute kidney injury via inhibiting caspase 1-mediated pyroptosis formation in rat

Background: Sepsis is a systemic inflammatory state associated with acute kidney injury (AKI) and high mortality. However, sepsis induced AKI cannot be efficiently prevented or cured using current antimicrobial therapies and supportive measures. We explored the therapeutic effect of newly developed fructose esters on sepsis-induced AKI (S-AKI). Methods: We used the surface plasmon resonance technique and ultrasensitive chemiluminescence analyzer to characterize the lipopolysaccharide (LPS)/endotoxin binding activity and antioxidant capability of fructose esters. We evaluated the degree of fructose ester gastrointestinal digestion using rat intestinal acetone powder. We examined the therapeutic effect of fructose esters on LPS-induced S-AKI by evaluating the blood and renal reactive oxygen species (ROS) amounts, Caspase 1 mediated pyroptosis, inflammation, microcirculation, and renal dysfunction. Results: Our data showed that the fructose esters are not easily hydrolyzed by the rat intestinal acetone powder implicating its high stability in the gastrointestinal tract. 1,6-dilauroyl-D-fructofuranose (FDL) dose-dependently scavenged H2O2 activity displayed a higher binding affinity to LPS than sialic acid and fructose did. LPS significantly enhanced Caspase 1 mediated pyroptosis and increased leukocyte infiltration, blood and renal ROS amount and BUN and creatinine level, whereas FDL significantly depressed these LPS-enhanced parameters. In addition, the increased plasma inflammatory cytokines levels using LPS could be reduced by intravenous fructose ester FDL treatment. Conclusion: Our data suggest that FDL with antioxidant H2O2 activity can neutralize LPS toxicity using a high binding affinity, and attenuate S-AKI by inhibiting Caspase 1 mediated pyroptosis resulting in ameliorating renal oxidative stress and dysfunction.

Carbon Nano-Dots based potentiometric sensor for the assay of the antiviral agent; Valacyclovir: In-Depth DFT Calculations, application to the pharmaceutical formulation and greenness assessment

Valacyclovir (VAL), as a prodrug to acyclovir antiviral agent, has recently held a lot of interest for its efficacy boosting owing to the significant improvement in bioavailability. This makes it a successful candidate in the management of herpes simplex strains as well as CORONA viruses. In this work a carbon nano dot-modified glassy carbon electrode (GCE) has been optimized as potentiometric sensor for the assay of VAL through a systematic approach. A mixture components of polyvinyl chloride (PVC) membrane have been selected and fine-tuned for optimum sensitivity and selectivity. The best results have been obtained by drop casting a blend in % w/w of PVC; 30.85, tricrasyl phosphate (TCP) as plasticizer; 64.32, phosphotungstic acid (PT) as cation exchanger; 1.61 and phosphorus – nitrogen-doped carbon nano-dots (PNCDs); 3.22 over the GCE. The density function theory (DFT) calculations have been applied to the optimized structures of VAL and the CDs and have proven high binding affinity of 46 kcal/mol dominated by π-π stacking and hydrogen bonding. The developed sensor has exhibited a swift response time of six seconds at a 5.00 pH value. The ICH guidelines have been applied to validate the optimized parameters. A good linearity range has been obtained from 1.18 × 10-3 down to 1.07 × 10-6 M for a correlation coefficient 0.9996 with a Nernstian slope of 33.16 mV/decade. The greenness has been assessed using the AGREE approach, giving a score of 0.8, which has indicated the environmental friendliness. An average % recovery of almost 99.00 % was obtained by application to the tablet formulations and furtherly it has been monitored by the standard addition method, giving recoveries varied from 98.00 and up to 102.00 % for relative standard deviation values (%RSD) less than 1.50 %, evidencing efficiency for application in the quality control laboratories.

Novel β-amyloid PET Imaging Study of [18F]92 in Patients with Cognitive Decline.

[18F]-4-((E)-(((E)-4-(2-(2-(2-Fluoroethoxy)ethoxy)ethoxy)benzylidene)-hydrazono)methyl)-N-methylaniline ([18F]92) is a novel positron emission tomography (PET) tracer previously reported to exhibit high binding affinity to aggregated β-amyloid (Aβ). This study aims to report a fully automated radiosynthesis procedure for [18F]92, explore its radioactive distribution in the brains of healthy subjects, and investigate its potential application value in the early diagnosis of Alzheimer's disease (AD). The fully automated radiosynthesis of [18F]92 was performed on the AllinOne module. Thirty one participants were recruited for this study. Dynamic [18F]92 PET imaging was conducted over 0-90 min period to assess time-activity curves (TAC) and standardized uptake value ratio (SUVR) curves in cognitively normal (CN) subjects. All participants were visually classified as either positive (+) or negative (-). Semiquantitative analyses of [18F]92 were performed by calculating SUVRs in different regions of interest. Furthermore, the study analyzed the relationships between global SUVR and plasma AD biomarkers, including Aβ42, Aβ40, P-tau181, and T-tau. The automated radiosynthesis of [18F]92 was completed within 50 min, yielding a radiochemical purity of greater than 95% and a radiochemical yield of 36 ± 3% (nondecay-corrected). Among the participants, 15 were estimated as Aβ (-) and 16 as Aβ (+). TACs indicated that [18F]92 rapidly crossed the blood-brain barrier within 10 min, followed by a rapid decrease, which then slowed down in the last 50-90 min. SUVR curves revealed that SUVR values stabilized around 60-70 min after injection and reached an equilibrium between 70 and 90 min, primarily in the cerebral cortex. SUVRs of Aβ (+) participants were significantly higher than those of Aβ (-) individuals within the cerebral cortex. In addition, Aβ42 and the Aβ42/Aβ40 ratio exhibited negative correlations with global SUVR, while plasma P-tau181 and the P-tau181/T-tau ratio displayed positive correlations with global SUVR. [18F]92 exhibits excellent pharmacokinetic properties in the human brain and can be synthesized automatically on a large scale. [18F]92 is a promising and reliable radiotracer for estimating Aβ pathology accumulation, providing valuable assistance in AD diagnosis and guiding clinical trials of therapeutic drugs.

Based on UHPLC-Q-TOF-MS and bioinformatics strategies, the potential allergens and mechanisms of allergic reactions caused by Danshen injection were explored.

The aim is to investigate the potential allergens and mechanisms underlying allergic-like reactions induced by Danshen injection (DSI). Utilizing ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS), metabolomics, and bioinformatics, we identified the key allergens, targets, and metabolic pathways involved in DSI-induced allergic-like reactions, validating binding efficiency through molecular docking and molecular dynamics. A total of 45 compounds were identified within DSI, with 24 compounds exhibiting strong binding activity to the MrgprX2 activation site. DSI was found to cause changes in 89 endogenous metabolites, including arachidonic acid, prostaglandins, and leukotrienes, primarily affecting pathways such as phenylalanine metabolism and arachidonic acid metabolism. The key allergens identified were Cryptotanshinone, Miltipolone, Neocryptotanshinone, Salvianolic acid B, and Isosalvianolic acid C, which primarily trigger allergic-like reactions by regulating upstream signaling targets such as ALOX5, PTGS1, PPARD, and LTB4R. Validation confirmed the high binding affinity and stability between key allergens and targets. These findings indicate that the allergic components in DSI primarily induce allergic-like reactions by modulating the aforementioned signaling targets, activating the AA metabolic pathway, promoting mast cell degranulation, and releasing downstream endogenous inflammatory mediators, subsequently eliciting allergic-like reactions.

Sturgeon (Acipenser schrenckii) spinal cord peptides: Antioxidative and acetylcholinesterase inhibitory efficacy and mechanisms

Providing antioxidants and targeting acetylcholinesterase (AChE) are key strategies in treating neurocognitive dysfunction. In this study, bioactive sturgeon (Acipenser schrenckii) spinal cord peptides (SSCPs) with antioxidant and AChE inhibitory potency were extracted and separated from sturgeon spinal cord by enzymatic hydrolysis and ultrafiltration, and targeted peptide PGGW was screened via computer simulated molecular docking. Further, the molecular dynamic interactions of the PGGW with superoxide dismutase (SOD) and AChE were analyzed, and the protective effect of PGGW on glutamate-induced PC12 cells in vitro was evaluated. The <3 kDa fraction of SSCPs displays the most potent antioxidative efficacy (1 mg/mL, DPPH•: 89.07%, ABTS+: 76.35%). Molecular dynamics simulation showed that PGGW was stable within AChE and tightly bound to residues SER203, PHE295, ILE294 and TRP236. When combined with SOD, the indole group of PGGW was stuck inside SOD, but the tail chain PGG fluctuated greatly outside. Surface plasmon resonance demonstrated that PGGW has a high binding affinity for AChE (KD = 1.4 mM) and 0.01 mg/mL PGGW provided good protection against glutamate-induced apoptosis. The findings suggest a promising strategy for drug research on neurodegenerative diseases.

Strong binding between nanoplastic and bacterial proteins facilitates protein corona formation and reduces nanoplastics toxicity

The interaction and combination of nanoplastics with microorganisms, enzymes, plant proteins, and other substances have garnered considerable attention in current research. This study specifically examined the interaction and biological effects of NPs and proteins. The findings indicated that the presence of externally wrapped proteins alters the original morphology and surface roughness of nanoplastics, leading to the formation of unevenly distributed coronas on the surface. This confirms that nanoplastics can interact with proteins to form protein coronas. The study characterized the adsorption behavior of bacterial proteins on unmodified, amino-modified, and carboxyl-modified nanoplastics using Langmuir and Freundlich isotherm models, showing that the adsorption process of the three nanoplastics on bacterial proteins was mainly controlled by chemisorption. Fluorescence spectroscopy revealed a higher binding affinity of unmodified nanoplastics. Nearly 40 % of the proteins in the protein corona of unmodified NPs are involved in metabolite production and electron transport processes. Nearly 50 % of the proteins in the protein corona of amino-modified NPs are involved in cellular metabolic processes, followed by enzymes that carry out redox reactions. The protein corona of carboxyl-modified NPs has the highest number of proteins involved in metabolic pathways, followed by proteins involved in energy-electron transfer. The formation of protein coronas on NPs with different surface modifications can reduce the toxicity of nanoplastics to bacteria to a certain extent compared to pure nanoplastics, especially amino-modified NPs, which show a significant increase in bacterial survival. The formation of protein coronas on NPs leads to varying degrees of decrease in bacterial ROS and MDA generation, with amino-modified NPs showing the most reduction; SOD and CAT exhibit varying degrees of increase and decrease. These findings not only advance our understanding of the biological impacts of NPs but also provide a basis for future in-depth investigations into the pathways of NP contamination in real environments.

In silico analysis of endocrine-disrupting potential of triclosan, bisphenol A, and their analogs and derivatives.

Owning to the increasing body of evidence about the ubiquitous exposure to endocrine disruptors (EDCs), particularly bisphenol A (BPA), and associated health effects, BPA has been gradually substituted with insufficiently tested structural analogs. The unmanaged excessive use of antimicrobial agents such as triclosan (TCS) during the COVID-19 outbreak has also raised concerns about its possible interferences with hormonal functions. The similarity of BPA and estradiol, as well as TCS and non-steroidal estrogens, imply that endocrine-disrupting properties of their analogs could be predicted based on the chemical structure. Hence, this study aimed to evaluate the endocrine-disrupting potential of BPA substitutes as well as TCS derivatives and degradation/biotransformation metabolites, in comparison to BPA and TCS based on their molecular properties, computational predictions of pharmacokinetics and binding affinities to nuclear receptors. Based on the obtained results several under-researched BPA analogs exhibited higher binding affinities for nuclear receptors than BPA. Notable analogs included compounds detected in receipts (DD-70, BTUM-70, TGSA, and BisOPP-A), along with a flame retardant, BDP. The possible health hazards linked to exposure to TCS and its mono-hydroxylated metabolites were also found. Further research is needed in order to elucidate the health impacts of these compounds and promote better regulation practices.

Larvicidal activity of β-Citral: An In-vitro and In-silico study to understand its potential against mosquito

Tropical and subtropical regions face millions of deaths from mosquito-borne illnesses yearly. Insecticides prevent transmission but pose health risks like dermatitis and allergies. The primary objective was to mitigate the recurring dependence on synthetic insecticides, thereby curbing the development of mosquito resistance. Leaves of Cymbopogon flexuosus (lemongrass) was collected from Mayurbhanj, India, processed, then extracted by steam distillation for essential oils & analyzed spectroscopically. Larvicidal assays were performed across varying concentrations, revealing the significant mortality induced by the Cymbopogon flexuosus extract against Anopheles stephensi larvae. 3D structure was modelled by using G protein-coupled receptors (GPCR) sequence and structural stability was also validated. After docking the binding free energy was determined from GPCR protein with β-citral complex. Molecular dynamics (MD) study was conducted on the docked pose that displayed an optimal interactome profile. The larvicidal assay at the 12th and 24th hour revealed the highest LC50 (lethal concentration) of 23.493 ppm and 19.664 ppm . β-Citral has a high binding affinity and an identifiable binding site, which suggests that it may play a larvicidal role in regulating the receptor's function by creating stable complexes with it. β-Citral from lemongrass oils has potential larvicidal activity and effective against GPCR family 1 of mosquito and highly effective repellents against mosquito-borne diseases.

Highly Sensitive and Selective Recognition of Zn2⁺ and Fe2⁺ Ions Using a Novel Thiophene-Derived Hydrazone Dual Fluorometric Sensor.

The selective detection of Zn2⁺ and Fe2⁺ ions is critical in environmental and biological studies. Schiff base chemosensors hold promise, but exploration of thiophene-derived variants remains limited. This work introduces a novel thiophene-derived Schiff base sensor (TBH), synthesized through the condensation reaction of thiophene-2-carboxaldehyde with benzil-bis-hydrazone, for the selective detection of Zn2⁺ and Fe2⁺ ions. TBH exhibits remarkable selectivity, with a significant 185-fold fluorescence enhancement for Zn2⁺ and complete quenching 99% for Fe2⁺, allowing for distinct detection of both ions. Notably, TBH demonstrates high binding affinity towards Zn2⁺ and Fe2⁺, even in the presence of competing cations, forming stable 1:1 complexes. This finding is supported by absorption and emission titration studies and FT-IR analysis as well. This easily synthesized, rapid and cost-effective sensor offers a promising approach for sensitive and differentiated dual detection of Zn2⁺ and Fe2⁺ in environmental and biological systems.

De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model

Artificial Intelligence (AI) techniques have made great advances in assisting antibody design. However, antibody design still heavily relies on isolating antigen-specific antibodies from serum, which is a resource-intensive and time-consuming process. To address this issue, we propose a Pre-trained Antibody generative large Language Model (PALM-H3) for the de novo generation of artificial antibodies heavy chain complementarity-determining region 3 (CDRH3) with desired antigen-binding specificity, reducing the reliance on natural antibodies. We also build a high-precision model antigen-antibody binder (A2binder) that pairs antigen epitope sequences with antibody sequences to predict binding specificity and affinity. PALM-H3-generated antibodies exhibit binding ability to SARS-CoV-2 antigens, including the emerging XBB variant, as confirmed through in-silico analysis and in-vitro assays. The in-vitro assays validate that PALM-H3-generated antibodies achieve high binding affinity and potent neutralization capability against spike proteins of SARS-CoV-2 wild-type, Alpha, Delta, and the emerging XBB variant. Meanwhile, A2binder demonstrates exceptional predictive performance on binding specificity for various epitopes and variants. Furthermore, by incorporating the attention mechanism inherent in the Roformer architecture into the PALM-H3 model, we improve its interpretability, providing crucial insights into the fundamental principles of antibody design.