Binding Affinity Research Articles

Comparative study of essential oil extraction from lime peel (Citrus amblycarpa Hassk. Ochse): Impact on chemical composition and bioactivities of anti-tyrosinase, anti-elastase, and antimicrobial properties

Essential oil is a natural substance widely utilized in the cosmetics industry. However, there has been no study on the cosmetic bioactivity of essential oil from the peel of Citrus amblycarpa Hassk. Ochse (CAEO). This study aimed to investigate the potential of CAEO, obtained through NaCl hydrodistillation (HD) and microwave-assisted hydrodistillation (MAHD), as an anti-tyrosinase, anti-elastase, and antibacterial agent, along with analyzing its chemical constituents. GC-MS analysis identified β-pinene (28.3%) and limonene (27.1%) as the main compounds in CAEO (HD), while limonene (13.75%) and citronellal (7.49%) predominated in CAEO (MAHD). The CAEO obtained from HD with 25% NaCl as the solvent exhibited significantly higher (p < 0.05) anti-tyrosinase (IC50 = 235.94 ± 1.34 μg/mL) and anti-elastase (IC50 = 41.59 ± 0.47 μg/mL) activities compared to the CAEO from the MAHD method. This result was consistent with the in silico pharmacological study, which revealed that limonene, the major component of CAEO, showed good binding affinity to the active sites of elastase and tyrosinase. The CAEO obtained from both methods exhibited strong and selective antibacterial activity in a disc diffusion assay against two bacteria associated with skin acne: Propionibacterium acnes ATCC 11827 (CAEO HD = 24.08 ± 5.85 mm) and Staphylococcus aureus ATCC 25923 (CAEO MAHD = 20.5 ± 0.27 mm). These results pave the way for further studies on the bioassay-guided isolation of CAEO to enhance its effectiveness as a cosmetic agent. Moreover, this study provides the first report indicating the potential of CAEO for development as a cosmetic agent.

Female contact sex pheromone recognition in the German cockroach (Blattella germanica) is mediated by two male antennae-enriched sensory neuron membrane proteins.

The German cockroach Blattella germanica is a notorious urban health pest that has developed resistance to multiple pesticides. Thus, novel non-lethal pest control agents are urgently needed. Olfaction interference via disruption of sex pheromone recognition-related genes offers a promising approach. The German cockroach has a unique courtship behavior in which female adults emit contact sex pheromones (CSPs) in response to antennal touching, which subsequently triggers distinctive male sex behavioral responses. Due to the limited volatility of CSPs, the molecular mechanisms underlying their recognition and the specific olfactory pathways activated remain poorly defined. Although the odorant receptor coreceptor (Orco) is critical for most insect olfaction, sensory neuron membrane proteins (SNMPs), in particular SNMP1, also play crucial roles in sex pheromone recognition in moths and flies. While multiple SNMP1 homologs have been identified in multiple insect species, they have yet to be fully functionally characterized in cockroaches. In this study, RNA-interference (RNAi)-mediated knockdown of BgerOrco reduced both the electrophysiology responses and courtship behaviors of males, indicating CSP perception proceeds via an olfaction pathway. Similar RNAi knockdown of BgerSNMP1e and BgerSNMP1d, which are predominantly expressed in male antennae, revealed critical roles in perceiving the major component of the Blattella germanica CSP blend. Unlike BgerSNMP1e, BgerSNMP1d was also found to function in the perception of the minor CSP component. Molecular docking analyses revealed no differences in the binding affinities of BgerSNMP1d for the major and minor CSP components, whereas the binding affinities of BgerSNMP1e displayed clear selectivity for the major component. Our results show that the olfactory pathway is critical for CSP recognition and that two male-enriched SNMP genes, BgerSNMP1e and BgerSNMP1d, are crucial factors mediating the male response to CSP stimulation in German cockroaches. This study lays a foundation for studying the mechanisms of CSP recognition and provides novel molecular targets with potential to be exploited as disruptors of courtship behavior. © 2024 Society of Chemical Industry.

Combination of Metabolomics and Bioinformatics to Reveal the Mechanism of Luteolin in the Treatment of Cervical Cancer.

The incidence of cervical cancer is high among women globally. The potential therapeutic efficacy of luteolin in the treatment of cervical cancer has been identified. Therefore, we aim to elucidate the mechanism of action of luteolin in the treatment of cervical cancer through a comprehensive approach that integrates metabolomics with bioinformatics. The first step involved the identification of differential metabolites through UHPLC-Q-Orbitrap-MS, which were then utilized for enrichment analysis of metabolic pathways and to determine the targets associated with these differential metabolites. Subsequently, the differential analysis and WGCNA were employed to identify DEGs and functional module genes respectively. The common targets were obtained by intersecting the results from the aforementioned three analyses, followed by conducting GO and KEGG pathway enrichment analysis on these targets. Subsequently, PPI networks were constructed using these common targets, and key targets were identified utilizing the MCC, EPC, Degree, Closeness Centrality, Betweenness Centrality, and Bottleneck algorithms in the CytoHubba plug-in. The subsequent steps involved the analysis of key genes for constructing a nomogram, conducting a ROC curve, examining content expression and survival analysis, and ultimately employing molecular docking to investigate the interaction between luteolin and crucial targets. The metabolomics analysis revealed the identification of a total of 45 distinct metabolites in this study, primarily associated with amino acid and nucleotide metabolism. The intersection of 773 differential metabolite targets, 3493 cervical cancer differential genes, and 3245 WGCNA-associated module genes yielded a set of 32 target genes associated with luteolin therapy for cervical cancer. The GO and KEGG pathway enrichment analysis also revealed that these targets were primarily associated with amino acid metabolism and nucleotide metabolism. The CytoHubba plug-in was utilized to identify three key genes (DMNT1, EZH2, and GMPS) through the application of multiple algorithms. Additionally, the datasets GSE63514, GSE67522, and GEPIA2 revealed a significant upregulation of all three genes in tumor tissue. ROC analysis demonstrated the good predictive ability of these three hub genes. Finally, the molecular docking results demonstrated the high binding affinity of luteolin towards DMNT1, EZH2, and GMPS. In conclusion, this study has unveiled the potential of luteolin in modulating amino acid and nucleotide metabolism for the treatment of cervical cancer, thereby providing a theoretical foundation for further investigation into the intricate association between luteolin and cervical cancer.

BSA/EGCG Binding Affinity Modified by Nanosecond Pulsed Electric Field

BSA/EGCG Binding Affinity Modified by Nanosecond Pulsed Electric Field

Synthesis, biological evaluation, and in silico studies of phenyl naphthalene-2-sulfonate derived thiosemicarbazones as potential carbonic anhydrase inhibitors.

A series of novel phenyl naphthalene-2-sulfonate-based thiosemicarbazones (5a-v) were synthesized and evaluated for their inhibitory activity against human carbonic anhydrases I and II (hCA I and hCA II). Compounds 5d and 5p demonstrated the highest inhibitory potency, with IC50 values of 4.32±0.02nM and 5.24±0.03nM for hCA I, and 3.89±0.01nM and 4.72±0.01nM for hCA II, respectively. Notably, compound 5d exhibited superior potency compared to the reference drug acetazolamide. The structure-activity relationship (SAR) analysis revealed that electron-withdrawing groups, particularly the dichlorophenyl group in 5d and 5p, enhanced inhibitory activity. Molecular docking and molecular dynamics simulations confirmed the high binding affinity of compound 5d, with docking scores of -9.7kcal/mol for hCA I and -9.5kcal/mol for hCA II. Stability in MD simulations further supported its potent inhibitory action. ADMET predictions suggested that compounds 5d and 5p have favorable pharmacokinetic profiles. In conclusion, phenyl naphthalene-2-sulfonate-based thiosemicarbazones, especially compound 5d, show strong potential as therapeutic agents targeting hCA I and hCA II.

The processing of shaking and standing improves the taste quality of summer black tea.

Shaking and standing (SS) enhances the aroma intensity and quality of black tea (BT). However, its contribution to the taste remains unknown, and the interaction mechanism between the aroma and taste perception of black tea is also undisclosed. Here, the metabolomics and sensory evaluation-assisted flavor analysis were employed to investigate the changes in non-volatiles induced by SS, and the interaction mechanism between aroma and taste perception. SSBT exhibited considerable reduced bitterness and astringency intensities compared to BT. Notably, the concentrations of contributing compounds such as catechins, proanthocyanidins, theaflavins, anthocyanins, and flavonol glycosides were decreased in SSBT. Sensory experiments further revealed that nine floral and sweet odorants in SSBT exhibited odor-enhancing interactions. Molecular docking validated the binding affinity and interaction forces between mono/di-ligands and OR1G1/OR52D1. Furthermore, the presence of the nine odorants exerted inhibitory effects on the bitterness and astringency of SSBT. These findings provide a novel perspective on the formation of flavor in SSBT.

Comprehensive study of Biginelli's compounds show antibacterial activity against Vibrio parahaemolyticus of two strains: In vitro and computational approaches.

This study addresses the critical challenges faced by global aquatic industries such as overfishing, habitat destruction, pollution, climate change, and unsustainable aquaculture practices. It focuses on developing effective solutions by synthesizing potent inhibitors against Vibrio parahaemolyticus of two strains namely: MTCC-451 (A) and Vp-S14 (B). Biginelli's compounds (B1-4) were identified as promising inhibitors with confirmed antibacterial activity through in silico and in vitro studies. Then virtual screening through ADMET, best correlation with regard to QSAR studies, the docking analysis is used to determine, the ligand B1 would be more favorable comparable with others for conducting bacterial studies and DFT calculations show that the optimized structure of ligand B1 has the best FMO values, MEP values and appropriate electronic structural state. This research study is very helpful and matches for "Antibacterial analysis". A total of 99 Biginelli compounds were selected for virtual screening including 2D-QSAR, ADME/T, molecular docking, and DFT calculations. The virtual screened compounds were synthesized then for biological studies. The four highlighted compounds (B1-4) with favorable ADME properties and strong binding affinities compared to gentamicin in both ADME and docking analysis respectively. Further analysis via DFT provided structural insights and active site identification. In vitro assays against pathogenic Vp strains demonstrated significant bactericidal activity, with MIC values of 1.25mg/ml (MTCC-451) and 1mg/ml (Vp-S14).

Molecular simulations reveal intricate coupling between agonist-bound β-adrenergic receptors and G protein.

G protein-coupled receptors (GPCRs) and G proteins transmit signals from hormones and neurotransmitters across cell membranes, initiating downstream signaling and modulating cellular behavior. Using advanced computer modeling and simulation, we identified atomistic-level structural, dynamic, and energetic mechanisms of norepinephrine (NE) and stimulatory G protein (Gs) interactions with β-adrenergic receptors (βARs), crucial GPCRs for heart function regulation and major drug targets. Our analysis revealed distinct binding behaviors of NE within β1AR and β2AR despite identical orthosteric binding pockets. β2AR had an additional binding site, explaining variations in NE binding affinities. Simulations showed significant differences in NE dissociation pathways and receptor interactions with the Gs. β1AR binds Gs more strongly, while β2AR induces greater conformational changes in the α subunit of Gs. Furthermore, GTP and GDP binding to Gs may disrupt coupling between NE and βAR, as well as between βAR and Gs. These findings may aid in designing precise βAR-targeted drugs.

Peripartum buprenorphine and oxycodone exposure impair maternal behavior and increase neuroinflammation in the brains of new mother rats

7 % of pregnant people use opioids. Opioid use during pregnancy can negatively impact maternal and offspring health. Medications for opioid use disorder (MOUD), commonly buprenorphine, are the recommended treatment for opioid use disorder during pregnancy to prevent cycles of withdrawal and relapse. In addition to effects on opioid receptors, opioids have strong binding affinity to toll-like receptor (TLR) 4, an immune cell receptor, and thereby impact neuroinflammatory signaling. We have previously shown that neuroimmune alterations are important for the display of maternal behavior. Here, we used a rodent model to assess the impact of chronic peripartum opioid exposure or MOUD on maternal caregiving and neuroinflammation in the postpartum brain. Female rats were exposed to vehicle (VEH), buprenorphine (BUP) to model MOUD, or oxycodone (OXY), to model peripartum drug use, before, during, and after pregnancy. Opioid exposure reduced gestation length and maternal weight gain. Postpartum maternal caretaking behaviors, including pup retrieval, huddling and nursing, and pup-directed sniffing and licking, were reduced in opioid-exposed mothers. Following behavioral testing, tissue was collected from brain regions important for maternal caretaking, including the prefrontal cortex (PFC), nucleus accumbens (NAc), preoptic area (POA), amygdala (AMY), and periaqueductal grey (PAG). Immunofluorescent labeling showed that BUP increased astrocyte labeling, while OXY increased microglia labeling in the PAG, but not other regions. Gene expression analysis also showed regional and treatment differences in immune transcripts. BUP and OXY increased TLR4 in the PFC. BUP increased TNF in the NAc but decreased IL1β in the POA. OXY increased CD68 in the POA, and IL1β, TNF, and TLR4 in the PAG. Together, these results provide novel evidence of peripartum neuroimmune alterations following chronic opioid exposure that could be mediating maternal care deficits. This work provides a foundation to explore the extent to which modulation of neuroimmune activation may be a potential intervention for caregiving deficits in mothers exposed to opioids during pregnancy.

Sodium Danshensu Alleviates Bone Cancer Pain by Inhibiting the Osteoclast Differentiation and CGRP Expression.

The morbidity of bone cancer pain (BCP) is on the rise, yet current treatments have limited analgesic efficacy. Sodium Danshensu (SDSS), or sodium 3-(3,4-dihydroxyphenyl)-DL-lactate, exhibits anti-inflammatory, anti-osteoporotic properties. Current research shows that bone cancer pain is closely related to the development of osteoclasts. To investigate the analgesic effects of SDSS on BCP in mice and explore the underlying mechanisms. Nociceptive behaviors in BCP mice were evaluated by paw withdrawal threshold (PWT) and limb using score (LUS). Network pharmacology, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, and molecular docking identified potential targets. Histological analyses, Western blot, RT-qPCR, ELISA, and immunofluorescence staining were performed on mice femurs. SDSS significantly increased PWT and LUS in BCP mice. Forty-three common targets were identified, with the estrogen signaling pathway showing the highest enrichment. Molecular docking analysis suggested a potential binding affinity between SDSS and ESRα. SDSS administration up-regulated ESRα expression and down-regulated RANKL, RANK, NFATc1, c-fos, TRAP, and Cathepsin K (CTSK). In addition, SDSS suppressed the abnormal increase of calcitonin gene-related peptide-positive (CGRP+) neural budding and expression in nerve endings, effects which were reversed by ESRa inhibitor ICI-182780. SDSS relieves bone cancer pain by inhibiting osteoclast activity, providing a potential new drug option for cancer pain patients.

Oxidative metabolism mechanism of terpenoid compound ZQ-8 by cytochrome P450 enzyme in Helicoverpa armigera.

In our previous research, we identified that treatment of Helicoverpa armigera with ZQ-8 led to upregulation of CYP450 genes. To clarify the metabolic pathway of ZQ-8, this study analyzed the expression of CYP450 genes and proteins in H. armigera after ZQ-8 treatment through transcriptomics and proteomics. Molecular docking, recombinant protein expression, and surface plasmon resonance techniques were employed to investigate the interactions between ZQ-8 and P450 proteins. The oxidative reduction related pathways were significantly enriched in H. armigera larvae treated with ZQ-8, with an increase in the expression of CYP6B2 and CYP6B6 genes. The CYP6B2 and CYP6B6 proteins exhibited significant expression following ZQ-8 treatment. ZQ-8 demonstrated rapid binding and stable dissociation characteristics with CYP6B6, characterized by a dissociation constant (KD) of 88.15μM. In contrast, ZQ-8 also showed rapid binding and dissociation with CYP6B2, but with a lower KD of 74.77μM indicating that CYP6B2 has a stronger binding affinity for ZQ-8 compared to CYP6B6, and is capable of oxidizing ZQ-8 to the corresponding carboxylic acid. This study provides a reference for the metabolism and mechanism of action of ZQ-8 as a potential drug molecule, laying the foundation for future drug design and optimization, paving the way for environmentally sustainable pest control strategies and reducing reliance on traditional chemical pesticides.

Mass spectrometric detection of neutrophil elastase cleaved corticosteroid binding globulin and its association with Asn347 site glycosylation, in septic shock patients.

Corticosteroid-binding globulin (CBG) modulates tissue cortisol availability via modification of cortisol:CBG binding affinity in response to multiple factors, including neutrophil elastase (NE) cleavage of the reactive centre loop (RCL), converting high affinity CBG (haCBG) to low affinity CBG (laCBG). In vitro, glycosylation of the RCL at Asn347 affects NE cleavage susceptibility. To date, no direct measurement of laCBG, which would verify NE cleavage, has been reported. To measure serum laCBG in septic shock patients by mass spectrometry to confirm NE cleavage in vivo, with Asn347 site glycosylation profiling to determine its impact on NE cleavage, and determine effect of %laCBG on septic shock clinical outcome. Serum from septic shock patients from a tertiary hospital intensive care unit was analysed by mass spectrometry for CBG affinity forms and Asn347 glycosylation profile, following CBG immunoprecipitation. Data was correlated with septic shock clinical outcome. N-terminal peptide of NE cleaved RCL (AVLQLNEEGVDTAGSTGV) was consistently detected in patient serum, although at low concentrations. Mean %laCBG/total CBG was 0.23% in septic shock (range=0.07-0.74%, SD=0.12%); in comparison healthy controls mean %laCBG was 0.04% (range 0.02-0.08%, SD=0.03%). There was a negative correlation between %laCBG and serum concentrations of CBG with triantennary Asn347 glycans; TS3 (r=-0.190, p=0.040) and TS3F (r=-0.252, p=0.006). NE cleaved CBG (laCBG) is present in septic shock patient serum, and %laCBG correlates with Asn347 glycosylation occupancy and composition. However, serum %laCBG did not correlate with septic shock clinical outcome.

Substrate and inhibitor specificity of Plasmodium nucleoside transporters ENT1 orthologs.

Malaria caused by Plasmodium infection poses a serious hazard to human health. Plasmodium falciparum equilibrative nucleoside transporter 1 (PfENT1), which mediates nucleoside uptake, is essential for the growth and proliferation of Plasmodium parasites, suggesting that PfENT1 is a potential antimalarial target. The promising compound GSK4 effectively inhibits the transport activity of PfENT1, thereby restraining the growth of Plasmodium parasites. However, it still needs to be clarified whether Plasmodium ENT1 orthologs have different selectivities for nucleosides and inhibitors. Here, we systematically compared the nucleoside selectivity of Plasmodium ENT1 orthologs from P.falciparum (PfENT1), Plasmodium berghei (PbENT1), and Plasmodium vivax (PvENT1), revealing that Plasmodium ENT1 orthologs present a distinct nucleoside recognition pattern. In addition, GSK4 robustly binds to PfENT1 and PvENT1 from two human-hosted Plasmodium parasites but has a weakened binding affinity for PbENT1 from mouse-hosted Plasmodium parasites. We further structurally optimized the inhibitor and generated three GSK4 analogs. One of the GSK4 analogs presented a slightly increased binding affinity for PfENT1. This optimization represents a promising advancement for antimalarial drug development, providing a novel foundation for future endeavors in antimalarial drug design.

Discovery of anti-tumor small molecule lead compounds targeting the SH3 domain of c-Src protein through virtual screening and biological evaluation.

c-Src, also known as cellular Src, is a non-receptor tyrosine kinase that plays a crucial role in various cellular processes, including cell proliferation, adhesion, and migration. Its dysregulation has been implicated in the development and progression of several diseases, particularly cancer. Current therapeutic agents targeting c-Src are primarily small molecules binding to its kinase domain. However, drug resistance often reduces the effectiveness of these drugs. The SH3 domain of c-Src is a highly conserved functional region with a low propensity for developing drug resistance, whereas there are no existing anti-cancer drugs specifically binding to this domain. In this study, structure-based virtual screening and thermal shift experimental verification identified three molecules that showed potent binding affinity with SH3 domain of c-Src. Subsequent kinase activity assay validated the inhibitory activity of these compounds against c-Src, with IC50 values ranging from 60.42 to 122.2nM. Next, cell-level assays and preliminary study were conducted to further evaluate the efficacy of the identified active compounds. In conclusion, the present work has provided new chemical templates as lead structures for the future development of new antitumor therapeutics targeting the c-Src SH3 domain to overcome drug resistance.

Potential Serotonin 5-HT2A Receptor Agonist of Psychoactive Components of Silene undulata Aiton: LC-MS/MS, ADMET, and Molecular Docking Studies.

Silene undulata is historically used for inducing vivid and prophetic lucid dreams, but limited information exists on its phytochemical composition and potential pharmacological properties. This study aimed to investigate the phytochemical composition of S. undulata through LC-MS/MS analysis and explore its potential serotonergic activity, which could support and confirm the traditional use of S. undulata as a dream-inducing plant. LC-MS/MS analysis was conducted on S. undulata extract, identifying 51 phytochemicals, including norharman, harmalol, harmaline, harmine, and ibogaine alkaloids. ADMET and Molecular docking investigations were employed to assess the serotonergic potential of these compounds. The analysis revealed the presence of β-carboline alkaloids, such as norharman, harmalol, harmaline, harmine, and ibogaine, within S. undulata extract. ADMET analysis showed that these compounds have a favourable pharmacokinetic properties. In addition, molecular docking investigations showed that harmaline (-8.90 Kcal/mol), harmalol (-8.56 Kcal/mol), and ibogaine (-8.75 Kcal/mol) exhibited binding affinities comparable to the control molecule, LSD (-9.14 Kcal/mol), indicating potential agonistic activity at serotonin 5-HT2A receptor. These findings provide insights into the potential therapeutic benefits of S. undulata, supporting its traditional use as a psychoactive plant. This study investigated the chemical constituents and potential serotonergic agonist activity of S. undulata for the first time. While promising, further research is necessary to uncover additional medicinal properties associated with the identified phytochemical components.

Comparative study of Alpha, Beta, and Omicron spike protein by computing the IR/Raman frequencies and UV-Vis adsorption – A computational analysis through DFT

The outbreak of COVID-19 coronavirus disease around the end of 2019 was a pandemic. The virus has been mutated and so many strains like Alpha, Beta, and Omicron are present in different parts of the world. Hence, timely detection technique is important to overcome the diagnostic challenges. Considering the need for this pandemic situation, we used a spectroscopy test methodology to distinguish different strains of Covid-19 by computing the infrared & Raman frequencies and the optical absorption data. Optimization of spike protein of Alpha, and Omicron mutations showed the high value of dipole moment (4.44, and 4.36) Debye, and polarizability [Alpha (233.62), Omicron (228.65)] indicating more bioactivity of Alpha and Omicron instead of Beta. Molecular electrostatic potential map exhibits the presence of electrophilic and nucleophilic region suggesting charge transfer of spikes to accept/donate electrons and hence the system increased reactiveness. UV-Vis absorption analysis also shows electronic transitions (σ to π∗ and π to π∗) due to that protein probe mechanism of Alpha and Omicron becomes increasingly become unsaturated thus confirming its easy binding ability to the target human protein as compared to binding affinity of Beta spike protein.

Identification of a Novel Alkaloid Zj6-11 as a Potent Inhibitor of Influenza Virus Infection via Repression of Virus-Induced Mitochondria-Dependent Apoptosis.

Influenza A virus (IAV) remains a major global public health threat, especially with the emergence of antiviral resistance, highlighting the urgent need for novel therapeutics. Alkaloids are known for their antiviral properties, and chemical synthesis has become a key strategy in developing new alkaloid compounds. In this study, we synthesized a series of novel alkaloids using the Ugi reaction and assessed their antiviral potential and mechanisms. Through screening and validation, Zj6-11 was identified as a promising compound that effectively inhibits IAV infection in vitro. Molecular docking and binding affinity assays showed that Zj6-11 binds with high affinity to IAV nucleoprotein (NP) and inhibits its interaction with nucleic acids. Further, in vitro nuclear translocation assays confirmed that Zj6-11 suppresses NP nuclear import. Mechanistically, Zj6-11 significantly inhibits IAV-induced apoptosis and mitigates mitochondrial membrane potential dysfunction. Zj6-11 also inhibits cytochrome c release, reduces the expression of cleaved Caspase-9 and Caspase-3, and suppresses IAV-induced apoptosis-inducing factor (Aif) expression, suppressing IAV-induced mitochondrial apoptosis. More importantly, Zj6-11 plays a crucial role in protecting mice from IAV infection and reducing IAV pathogenicity. Our study provides mechanistic insights into Zj6-11's control of IAV infection in vitro and in vivo, offering new perspectives for antiviral therapy development.

Argonaute protein assisted drug discovery for miRNA-181c-5p and target gene ATM translation repression: a computational approach.

The miRNA binds to AGO's seed region, prompting the exploration of small molecules that can offset miRNA repression of target mRNA. This miRNA-181c-5p was found to be upregulated in the chronic traumatic encephalopathy, a prevalent neurodegenerative disease in contact sports and military personals. The research aimed to identify compounds that disrupt the AGO-assisted loop formation between miRNA-181c-5p and ATM, consequently repressing the translation of ATM. Target genes from commonly three databases (DIANA-microT-CDS, miRDB, RNA22 and TargetScan) were subjected to functional annotation and clustering analysis using DAVID bioinformatics tool. Haddock server were employed to make miRNA-181c-5p:ATM-AGO complex. A total of 2594 small molecules were screened using Glide XP based on their highest binding affinity towards the complex, through a three-phase docking approach. The top 5 compounds (DB00674-Galantamine, DB00371-Meprobamate, DB00694-Daunorubicin, DB00837-Progabide, and DB00851-Dacarbazine) were further analyzed for stability in the miRNA-181c-5p:ATM-AGO-ligand complex interaction using GROMACS (version 2023.2). Hence, these findings suggest that these molecules hold potential for facilitating AGO-assisted repression of ATM gene translation.

The molecular mechanism of transforming red light signal to (E)-β-caryophyllene biosynthesis in Arabidopsis.

It is known that red light irradiation enhances the biosynthesis of (E)-β-caryophyllene in plants. However, the underlying mechanism connecting red light to (E)-β-caryophyllene biosynthesis remains elusive. This study reveals a molecular cascade involving the phyB-PIF4-MYC2 module, which regulates (E)-β-caryophyllene biosynthesis in response to the red light signal in Arabidopsis thaliana. In this module, phyB positively regulates (E)-β-caryophyllene biosynthesis under red light, whereas PIF4 negatively regulates it; both regulations require the involvement of MYC2, a transcription factor that can bind directly to the promoter of the TPS21 gene which encodes (E)-β-caryophyllene synthase. Importantly, protein-protein and protein-DNA interaction assays show that PIF4 reduces the binding affinity of MYC2 to the TPS21 promoter through direct interaction with MYC2. We propose that the phyB-PIF4-MYC2 module represents a universal mechanism linking red light to sesquiterpene biosynthesis in plants.

Impact of vascular Ehlers-Danlos Syndrome-associated Gly substitutions on structure, function, and mechanics using bacterial collagen.

Vascular Ehlers-Danlos syndrome (vEDS) arises from mutations in collagen-III, a major structural component of the extracellular matrix (ECM) in vascularized tissues, including blood vessels. Fibrillar collagens form a triple-helix that is characterized by a canonical (Gly-X-Y)n sequence. The substitution of another amino acid for Gly within this conserved repeating sequence is associated with several hereditary connective tissue disorders, including vEDS. The clinical severity of vEDS depends on the identity of the substituted amino acid and its location. In this study, we engineered recombinant bacterial collagen-like proteins (CLPs) with previously reported Gly→X (X=Ser or Arg) vEDS substitutions within the integrin-binding site. Employing a combination of biophysical techniques, enzymatic digestion assays, integrin binding affinity assays, and computational modeling, we assessed the impact of Gly→X substitutions on structure, stability, function, and mechanical properties. While constructs with Ser or Arg substitutions maintained a triple-helix structure, Arg substitution significantly reduced global thermal stability, heightened susceptibility to trypsin digestion, and altered integrin α2-inserted (α2I) domain binding. Molecular dynamics (MD) simulations also demonstrated distinct effects of different Gly substitutions on the triple-helix structure - Arg substitutions induced notable bulging at the substitution site and disrupted interchain hydrogen bonds compared to Ser substitutions. Additionally, steered MD simulations revealed that Arg substitution led to a significant decrease in the Young's modulus of the triple-helix. Bacterial CLPs have proved to be a powerful model for studying the underlying mechanisms of vEDS-causing mutations in collagen-III. Serine and arginine substitutions differentially perturb cell-matrix interactions and ECM in a manner consistent with clinical vEDS severity.