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Aims: This study evaluated the use of machine learning to leverage drug absorption, distribution, metabolism and excretion (ADME) data together with physicochemical and pharmacological data to develop a novel anticholinergic burden scale and compare its performance to previously published scales. Methods: Experimental and in silico ADME, physicochemical and pharmacological data were collected for antimuscarinic activity, blood–brain barrier penetration, bioavailability, chemical structure and P‐glycoprotein (P‐gp) substrate profile. These five drug properties were used to train an unsupervised model to assign anticholinergic burden scores to drugs. The model performance was evaluated through 10‐fold cross‐validation and compared with the clinical Anticholinergic Cognitive Burden (ACB) scale and nonclinical Anticholinergic Toxicity Scores (ATS) scale, which is based primarily on muscarinic binding affinity. Results: In silico software (ADMET Predictor) used for screening drugs for their blood–brain barrier (BBB) penetration correctly identified some drugs that do not cross the BBB. The mean area under the curve for the unsupervised and ACB scale based on the five selected variables was 0.76 and 0.64, respectively. The unsupervised model agreed with the ACB scale on the classification of more than half of the drugs (49 of 88) agreed on the classification of less than half the drugs in the ATS scale (12 of 25). Conclusions: Our findings suggest that the commonly used ACB scale may misclassify certain drugs due to their inability to cross the BBB. By contrast, the ATS scale would misclassify drugs solely depending on muscarinic binding affinity without considering other drug properties. Machine learning models can be trained on these features to build classification models that are easy to update and have greater generalizability. [ABSTRACT FROM AUTHOR]

Antimicrobial photodynamic therapy (aPDT) is a promising approach to combat antibiotic resistance in endodontic infections. It eliminates residual bacteria from the root canal space and reduces the need for antibiotics. To enhance its effectiveness, an in silico and in vitro study was performed to investigate the potential of targeted aPDT using natural photosensitizers, Kojic acid and Parietin. This approach aims to inhibit the biofilm formation of Enterococcus faecalis, a frequent cause of endodontic infections, by targeting the Ace and Esp proteins. After determining the physicochemical characteristics of Ace and Esp proteins and model quality assessment, the molecular dynamic simulation was performed to recognize the structural variations. The stability and physical movement of the protein-ligand complexes were evaluated. In silico molecular docking was conducted, followed by ADME/Tox profiling, pharmacokinetics characteristics, and assessment of drug-likeness properties of the natural photosensitizers. The study also investigated the changes in the expression of genes (esp and ace) involved in E. faecalis biofilm formation. The results showed that both Kojic acid and Parietin complied with Lipinski's rule of five and exhibited drug-like properties. In silico analysis indicated stable complexes between Ace and Esp proteins and the natural photosensitizers. The molecular docking studies demonstrated good binding affinity. Additionally, the expression of the ace and esp genes was significantly downregulated in aPDT using Kojic acid and Parietin with blue light compared to the control group. This investigation concluded that Kojic acid and Parietin with drug-likeness could efficiently interact with Ace and Esp proteins with a strong binding affinity. Hence, natural photosensitizers-mediated aPDT can be considered a promising adjunctive treatment against endodontic infections. [ABSTRACT FROM AUTHOR]

BACKGROUND: Rice‐based distillers' spent cake (RDSC), a by‐product of the Chinese liquor (Baijiu) industry, is a potential source of angiotensin‐converting enzyme (ACE) inhibitory peptide. Since ACE plays a crucial role in controlling hypertension, inhibition of ACE has been widely emphasized. The ACE inhibitory active peptide derived from by‐products of food has been recognized as a safer and cheaper inhibitor. RESULTS: Aimed to discover ACE‐inhibiting active peptides in RDSC. Hydrolysis of RDSC by alcalase for 4 h followed by ultrafiltration yielded low‐molecular‐weight (< 3 kDa) fractions. Subsequently, a comprehensive method using a combination of liquid chromatography quadrupole time‐of‐flight mass spectrometry (LC‐Q‐TOF‐MS) and LC‐Q‐Exactive‐MS to identify the novel short peptides (3–5 amino acids residues; n = 7) and medium‐sized peptides (more than 6 amino acids residues; n = 6). In vitro activity assay showed that the peptides KPFFPGL, GFPRPLL, GPPGVF, and VGK exhibited the highest activity with inhibitory concentration of 50% (IC50) of 11.63, 12.34, 19.55, and 33.54 μmol L−1. Molecular docking reveal that the active and inactive sites (Glu123, Asp121, Arg522, and Lys118) play important roles in enhancing the ACE inhibitory activity of peptides. CONCLUSION: Here we report a comprehensive method that effectively extracted and identified the bioactive peptides from RDSC. Four highly active novel peptides may be the most promising candidates for functional foods against hypertension, provide significant information for enhancing value of rice‐based distilled by‐products. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Objectives: Oxidative stress is implicated in several metabolic cascades involved in glucose control. Hence, investigating antioxidant and antidiabetic activities is crucial for discovering an effective diabetes mellitus (DM) agent. This study was aimed at probing the therapeutic efficacy of hydro-ethanolic extract of Combretum paniculatum (HECP) and gas chromatography-flame ionization detector (GC-FID)-identified phytochemicals as novel agents for DM. Methods: We determined the total phenols, flavonoids, and antioxidant vitamins in HECP using standard methods. A GC-FID was used to decipher phytochemicals of HECP. The antioxidant and antidiabetic activities of HECP were assessed using in vitro and in silico approaches. Results: The results revealed that HECP is affluent in phenols, flavonoids, and vitamin E and demonstrated engaging antioxidant activities in 1,1-diphenyl-2-picryl-hydroxyl (DPPH; IC50 = 0.83 µg/mL), thiobarbituric acid-reactive substances TBARS; IC50 = 2.28 µg/mL), and ferric-reducing antioxidant power assay (FRAP; IC50 = 2.89 µg/mL). Compared with the reference drug, acarbose, HECP exhibited good α-amylase and α-glucosidase inhibitory capacity, having IC50 values of 14.21 and 13.23 µg/mL, respectively, against 13.06 and 11.71 µg/mL recorded for acarbose. More so, the extract's top 6 scoring phytochemicals (rutin, kaempferol, epicatechin, ephedrine, naringenin, and resveratrol) had strong interactions with amino acid residues within and around α-amylase and α-glucosidase active site domains. All the compounds but rutin had favourable drug-like characteristics, pharmacokinetics, and safety profiles when compared with acarbose. Conclusion: Altogether, our results vindicate the use of this herb in treating DM locally and reveal that it has pharmaceutically active components that could be used as novel leads in the development of DM drugs. [ABSTRACT FROM AUTHOR]

Background: Lipocalin-2 (LCN2), a neutrophil gelatinase-associated protein, plays an important role in iron homeostasis, infection, and inflammation. Polymorphism in the LCN2 gene is linked to various diseases such as cardiovascular disease, renal damage, and colorectal and pancreatic cancer. Identifying deleterious functional non-synonymous SNPs in the LCN2 gene is crucial in understanding how these genetic variations affect its structure and function. Methods: Several in silico tools such as SIFT, Polyphen-2, PROVEAN, PREDICT SNP, MAPP, and SNAP2 followed by I-MUTANT 2.0, MUpro, ConSurf, and NetsurfP-2.0, secondary structure of the protein by SOPMA and PSIPRED, while its interaction with other genes and proteins was analyzed using GeneMANIA and STRING, respectively, and AlphaFold for protein's 3D structure prediction. Results: The study identified 6 potentially harmful nsSNPs (rs11556770, rs139418967, rs142623708, rs200107414, rs201365744, rs368926734) and their structure and function were analyzed using prediction tools. I-MUTANT 2.0 predicted an increase in stability with the nsSNPs rs139418967, while the other shows decrease in protein stability with the 6 nsSNPs (rs11556770, rs139418967, rs142623708, rs200107414, rs201365744, rs368926734) which was validated using MUpro. ConSurf identified the 6 high-risk nsSNPs to be in the conserved regions of the protein. The result showed that rs11556770, rs139418967, rs142623708, rs200107414, rs201365744, and rs368926734 were found to be highly conserved and the variant amino acids. According to NetsurfP-2.0 server, the result showed that rs11556770 (Q39H), rs139418967 (L6P), rs368926734 (Y135H) were predicted to be exposed and rs142623708 (M71I), rs200107414 (Y52C), rs368926734 (Y135) were buried. The PSIPRED server analysis indicated that the predominant secondary structure was a strand, with lesser occurrences of coil and helix. Conclusion: Overall, the study identified detrimental nsSNPs of LCN2 using computational analysis which could be used for large population-based investigations and diagnosis. [ABSTRACT FROM AUTHOR]

Fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), a threat to maize production systems, is a polyphagous pest of global significance. There is no registered bioinsecticide of botanical origin to provide green remedy against this pest of concern. The present study reports for the first time the potency of the polar and non-polar bioinsecticidal leads sourced from Lippia alba (Mill.) N.E. Br. leaves. Shade-dried leaves of L. alba were extracted and evaluated; based on preliminary bioassay, the ethyl acetate leaf extract of L. alba (LEAE) was found to be the most potent against FAW in the in vitro and in vivo studies. Ultraperformance liquid chromatography-quadrupole time-of-flight-mass spectrometric (UPLCQToF-MS) analysis of LEAE revealed the rich chemical profile of 28 compounds, dominated by flavones, namely, naringenin, trihydroxy-dimethoxy flavone, and dihydroxy-trimethoxy flavone. Among others, glycosides, such as clerodendrin, calceolarioside E, forsythoside B, geniposide, and martynoside, and glucuronides, such as luteolin-7-diglucuronide, tricin-7-O-glucuronide, and luteolin-7-Oglucuronide, were also identified. LEAE exhibited exceptionally high in vitro [LC50 = 6,900 parts per million (ppm)] and in vivo (computed as damage score on a scale of 1-9) insecticidal activity against S. frugiperda, with no phytotoxicity at a dose as high as 20 times of LC50. LEAE also exhibited significant antifeedant, ovicidal, and growth regulatory activity at the 70-16,000 ppm (w/v) concentration range. In silico assessment revealed strong binding of martynoside, calceolarioside E, and forsythoside B with acetylcholinesterase-, sodium-, and chloride-dependent gaminobutyric acid (GABA) receptor and ryanodine receptor, respectively, facilitated by hydrogen bonds (conventional and C-H bonds) stabilized by hydrophobic pi-sigma, pi-pi stacked, pi-alkyl, and alkyl interactions. The present study established L. alba as a potential bioresource and secondary metabolite enriched LEAE as bioinsecticide for further product development. [ABSTRACT FROM AUTHOR]

Plant-derived phytochemicals from medicinal plants are becoming increasingly attractive natural sources of antimicrobial and antiviral agents due to their therapeutic value, mechanism of action, level of toxicity and bioavailability. The continued emergence of more immune-evasive strains and the rate of resistance to current antiviral drugs have created a need to identify new antiviral agents against SARS-CoV-2. This study investigated the antiviral potential of balsaminol, a bioactive compound from Momordica balsamina, and its inhibitory activities against SARS-CoV-2 receptor proteins. In this study, three Food and Drug Administration (FDA) COVID-19 approved drugs namely; nirmatrelvir, ritonavir and remdesivir were used as positive control. Molecular docking was performed to determine the predominant binding mode (most negative Gibbs free energy of binding/ΔG) and inhibitory activity of balsaminol against SARS-CoV-2 receptor proteins. The pharmacokinetics, toxicity, physicochemical and drug-like properties of balsaminol were evaluated to determine its potential as an active oral drug candidate as well as its non-toxicity in humans. The results show that balsaminol E has the highest binding affinity to the SARS CoV-2 papain-like protease (7CMD) with a free binding energy of − 8.7 kcal/mol, followed by balsaminol A interacting with the spike receptor binding domain (6VW1) with − 8.5 kcal/mol and balsaminol C had a binding energy of − 8.1 kcal/mol with the main protease (6LU7) comparable to the standard drugs namely ritonavir, nirmatrelvir and remdesivir. However, the ADMET and drug-like profile of balsaminol F favours it as a better potential drug candidate and inhibitor of the docked SARS-CoV-2 receptor proteins. Further preclinical studies are therefore recommended. [ABSTRACT FROM AUTHOR]

Integrated bioinformatics tools have created more efficient and robust methods to overcome in vitro challenges and have been widely utilized for the investigation of food proteins and the generation of peptide sequences. This study aimed to analyze the physicochemical properties and bioactivities of novel peptides derived from hydrolyzed milkfish (Chanos chanos) protein sequences and to discover their potential angiotensin-converting enzyme (ACE)- and dipeptidyl peptidase-4 (DPPIV)-inhibitory activities using machine learning-based tools, including BIOPEP-UWM, PeptideRanker, and the molecular docking software HADDOCK 2.4. Nine and three peptides were predicted to have ACE- and DPPIV-inhibitory activities, respectively. The DPPIV-inhibitory peptides were predicted to inhibit the compound with no known specific mode. Meanwhile, two tetrapeptides (MVWH and PPPS) were predicted to possess a competitive mode of ACE inhibition by directly binding to the tetra-coordinated Zn ion. Among all nine discovered ACE-inhibitory peptides, only the PPPS peptide satisfied the drug-likeness analysis requirements with no violations of the Lipinski rule of five and should be further investigated in vitro. [ABSTRACT FROM AUTHOR]

The antioxidant action of terngymnoside C (1) and hydroxytyrosol-1-glucoside (2), isolated for the first time from the flower buds of Ternstroemia lineata, as well as katsumadin (3), obtained from the seedless fruits, was evaluated using ABTS•+ and H2O2–Saccharomyces cerevisiae models. In silico docking analysis of 1, 2, and 3 determined their affinity forces to the aquaporin monomers of the modeled S. cerevisiae protein 3 (AQP3) and human protein 7 (AQP7) channels that regulate the H2O2 cell transport. The ABTS•+ antiradical capacity of these compounds showed IC50 values of 22.00 μM (1), 47.64 μM (2), and 73.93 μM (3). The S. cerevisiae antioxidant assay showed that at 25 µM (1) and 50 µM (2 and 3), the cells were protected from H2O2-oxidative stress. These compounds, together with quercetin and vitamin C, were explored through the modeled S. cerevisiae AQP3 and human AQP7 by molecular docking analysis. To explain these results, an antioxidant mechanism for the isolated compounds was proposed through blocking H2O2 passage mediated by aquaporin transport. On the other hand, 1, 2, and 3 were not cytotoxic in a panel of three cancer cell lines. [ABSTRACT FROM AUTHOR]

The mitigation of cadmium (Cd) pollution, a significant ecological threat, is of paramount importance. Pseudomonas aeruginosa harbors 2 Cd resistance genes, namely, cadR and cadA. Presently, our focus is on the identification and characterization of the cation-transporting P-type ATPase (cadA) in Pseudomonas aeruginosa BC15 through in silico methods. The CadA protein and its binding capacities remain poorly understood, with no available structural elucidation. The presence of the cadA gene in P aeruginosa was confirmed, showing a striking 99% sequence similarity with both P aeruginosa and P putida. Phylogenetic analysis unveiled the evolutionary relationship between CadA protein sequences from various Pseudomonas species. Physicochemical analysis demonstrated the stability of CadA, revealing a composition of 690 amino acids, a molecular weight of 73 352.85, and a predicted isoelectric point (PI) of 5.39. Swiss-Model homology modelling unveiled a 33.73% sequence homology with CopA (3J09), and the projected structure indicated that 89.3% of amino acid residues were situated favourably within the Ramachandran plot, signifying energetic stability. Notably, the study identified metal-binding sites in CadA, namely, H3, C30, C32, C35, H48, C89, and C106. Docking studies revealed a higher efficiency of Cd binding with CadA compared to other heavy metals. This underscores the crucial role of N-terminal cysteine residues in Cd removal. It is evident that CadA of P aeruginosa BC15 plays a crucial role in Cd tolerance, rendering it a potential microorganism for Cd toxicity bioremediation. The structural and functional elucidation of CadA, facilitated by this study, holds promise for advancing cost-effective strategies in the remediation of cadmium-contaminated environments. [ABSTRACT FROM AUTHOR]

The manuscript analyzes potential pre-mRNA biomarkers of Myasthenia gravis (MG) in thymoma in silico. GSE11967 data set and platform5188 from the Gene Expression Omnibus database apply for data preprocessing, normalization, and quality control. Quality metrics indicated high overall data integrity, with no significant outliers or batch effects detected. Differential expression analysis (DEG.) uses the limma package in R. We compared thymoma samples to normal thymus tissue to identify DEGs. The significance criteria are adjusted p -value <0.05 and a |log2 fold change| > 1. Functional enrichment and pathway analysis, ontology analysis, and KEGG pathway analysis further investigate the potential underlying biological processes. Despite the extensive use of gene expression profiling for identifying potential biomarkers and therapeutic targets, this study identifies DEGs ENSG00000112345 and ENSG00000234567 and pathways like hsa04110, hsa03013 and hsa04115 in thymoma with MG compared to normal thymus tissue using the GSE11967 dataset Plots like UMAP, Boxplot, Expression density and Mean variance demonstrate differential expression in disease and control group. The GSE11967 data set shows the presence of significant DEG and pathways in thymoma-associated MG tissue, compared to healthy tissue. A broader and integrative approach is needed to understand the complex expression biomarkers in thymoma in MG patients and other regulatory mechanisms that may contribute to the disease by multi-omic approaches. [ABSTRACT FROM AUTHOR]

Background: Although potato virus Y (PVY) is the most serious virus-infecting potato plants worldwide, the losses concurred by it remain unmanageable due to the lack of efficient anti-PVY agents. Hence, the objective of this study was to assess the antiviral properties of secondary metabolite compounds obtained from culture filtrates of four Trichoderma spp. isolates. The assessment was conducted using computational methods, including molecular docking, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis, as well as molecular dynamics simulations. The aim was to develop novel and effective agents for combating PVY. Results: The GC–MS analysis of the studied Trichoderma spp. secondary metabolites revealed 24 compounds with relative amounts exceeding 10%. Molecular docking was then performed using MOE software to evaluate the activity of these compounds against the PVY protein coat (PDB-ID: 6HXX). Ningnanmycin and ribavirin, known plant virus inhibitors, were employed as reference ligands for comparison. Among the compounds tested, C9, C10, C13, and C19 exhibited superior docking scores, root mean square deviation (RMSD) values, and binding modes compared to the reference ligands. In addition, these compounds successfully passed the ADMET analysis. Further investigation focused on compounds C13 and C19, which underwent in-depth analysis through MDs for 100 ns. The MDs trajectories demonstrated that both complexes exhibited favorable stability, compactness, and binding modes throughout the simulation period. However, the C19/PVY-CP complex outperformed the C13 complex in all calculated parameters such as RMSD, root mean square fluctuation (RMSF), radius of gyration (RoG), solvent-accessible surface area (SASA), and intermolecular hydrogen bonds. Interestingly, these findings aligned with the results obtained from the docking analysis, indicating that C9 and C10 possess high potential against PVY, as they exhibited binding modes like that of C19. Conclusion: These promising outcomes provide a solid foundation for considering the potential use of compounds C9, C10, C13, and C19 as antiviral agents. Further experimental validation and in-depth studies are warranted to assess the efficacy and safety of these compounds and their potential as antiviral therapeutics. To our knowledge, this is the first report to study the biological activities of the Trichoderma-based bioactive compounds against PVY using computational techniques. [ABSTRACT FROM AUTHOR]

Objectives: Litter size is a crucial economic factor in the sheep industry. Several factors and genes influence litter size, making the identification of genes or loci involved a genetic challenge. Gonadotropin-inhibitory hormone (GnIH) is one of several genes that influence sheep's reproductive traits. Thus, this study aimed to investigate whether variations in the GnIH gene affect the reproductive performance of Awassi and Hamdani ewes. Methods: DNA was extracted from 99 single-progeny ewes and 101 twin ewes. The polymerase chain reaction (PCR) produced amplicons of 262 bp, 275 bp, and 284 bp from exons 1, 2, and 3 of the GnIH gene. Single-strand conformational polymorphism (SSCP) technique was used for genotyping experiments. Sequencing and in silico analysis were performed on each set of SSCP-resolved bands. Results: Two genotypes of 262 bp amplicons were found: TT and TC. Sequence analysis revealed a novel missense mutation in the TC genotype at position c.122T>C. Five in silico tools were used to assess the impact of this mutation on GnIH protein structure, function, and stability, all of them demonstrated a deleterious effect. An analysis of statistical data revealed a strong correlation between the c.122T>C single-nucleotide polymorphism (SNP) and reproductive performance. Ewes with the SNP 122T>C exhibited a significant increase in litter size, twinning rates, lambing rates, and days to lambing when compared with ewes with the TT genotype. A lower number of lambs were born to ewes with the TT genotype than those with the TC genotype. Conclusion: These results concluded that the c.122T>C SNP variant positively influences the reproductive performance of Awassi and Hamdani sheep. Sheep that carry the c.122T>C SNP show higher litter size and increased productivity. [ABSTRACT FROM AUTHOR]

Background: Ceranib-2, an acid ceramidase (AC) inhibitor, can inhibit cancer cell proliferation and tumor development. However, poor water solubility and low cellular bioavailability limit its efficacy in cancer treatment. Methods and results: This study aimed to investigate the cell death induced by ceranib-2 and its solid lipid nanoformulation (ceranib-2-SLN) produced by the hot homogenization technique and the synergistic relationship between ceramide and telomerase in vitro and in silico. Furthermore, this study proved the possible mechanism of ceranib-2-induced AC inhibition by in silico studies. The effective cytotoxic concentrations of ceranib-2, telomerase level, and changes in ceramide levels were measured by MTT colorimetric cytotoxicity assay, ELISA, and LC/MS/MS methods, respectively. TEM results showed that ceranib-2-SLN was 13-fold smaller than the size of ceranib-2. Ceranib-2 and ceranib-2-SLN had IC50 concentrations of 31.62 (± 2.1) and 27.69 (± 1.75) µM in A549, and 48.79 (± 1.56) and 67.98 (± 2.33) in Beas-2B cells. These compounds simultaneously increased ceramide levels and decreased telomerase levels in A549 cells. Ceranib-2 increased telomerase levels while decreasing ceramide levels in Beas-2B cells. It was shown how the synergistic impact of ceranib-2-induced ceramide production and ceramide-induced telomerase level reduction on cytotoxicity in A549 cells. Conclusions: Ceranib-2-SLN was discovered to be more cytotoxic on cancer cells than ceranib-2, suggesting that it could be a promising option for the development of a new anti-cancer agent. [ABSTRACT FROM AUTHOR]

Background and Aims: Fungicides, particularly triazoles, are of global concern for pesticide contamination because of their widespread use. This study focuses on estimating the carcinogenicity and mutagenicity of 15 commonly used triazole fungicides. Methods: In silico prediction tools such as ProTox-II, Toxtree, Lazar, and VEGA were used to predict mutagenicity and carcinogenicity. Results: All compounds were predicted to be “non-mutagenic” by ProTox-II, Toxtree, and Lazar. However, the CONSENSUS of VEGA identified epoxiconazole and prothioconazole as “mutagenic." Regarding carcinogenicity predictions, ProTox-II indicated non-carcinogenicity for all compounds, whereas Toxtree and VEGA (ISS) raised structural alerts for 10 compounds. In addition, Lazar predicted carcinogenicity for tebuconazole, paclobutrazol, and penconazole. It is worth noting that the results exhibit variable reliability, emphasising the need for further investigation and validation. Conclusion: In silico tools proved valuable for predicting the toxicity of triazole fungicides, emphasising the need for additional data. Although the study categorises compounds as non-mutagenic, some exhibit structural alerts for potential carcinogenicity. This strategic approach contributes to pesticide risk assessment by highlighting the role of computational models in advancing our understanding of the health impacts associated with pesticide exposure. [ABSTRACT FROM AUTHOR]

Diabetes affects 537 million adults globally, with 19.47 million cases in Indonesia. It arises from insufficient or ineffective insulin production, leading to complications like nephropathy. Due to the adverse effects of conventional medications, there is a growing need for safer alternatives. Functional foods and bioactive compounds show promise in managing diabetes. One such alternative is rice. Indonesia boasts a unique rice variety known as Pulu Mandoti, exclusively cultivated in the Enrekang District, Makassar, Indonesia. This delightful red rice variant offers numerous nutritional benefits. Unlike white rice, red rice is abundant in essential nutrients such as calcium, zinc, magnesium, protein, and fiber. The study focused on Pulu Mandoti, exploring its potential for antidiabetic and antioxidant activities using LC-MS analysis. Twelve (12) compounds were identified within the 1.23-14.41-min retention time range, with Compound 11 (2,2'-methylenebis(dibenzo[b,d]thiophene)) showing the strongest antioxidant potential compared to vitamin C. In molecular docking, Compound 11 exhibited the lowest binding affinity for both alpha-amylase and alpha-glucosidase (-10.5 and -8.7 kcal/mol, respectively), whereas acarbose displayed the highest binding affinity. For antioxidant analysis, Compounds 11 and 5 demonstrated the lowest binding affinities for NADPH oxidase and xanthine oxidoreductase, respectively, whereas vitamin C showed the highest. The coefficient values for drug properties similarity ranged from 0.40-0.76 for antidiabetic drugs, with Compound 5 displaying the highest coefficient value (0.76) and from 0.41-0.68 for antioxidants, with the highest value observed for antioxidant peptide A acetate. [ABSTRACT FROM AUTHOR]

Nanotechnology can contribute significantly to the aquaculture sector for a wide range of applications. In this study, silica nanoparticles were prepared from beach sand and characterized. The XRD pattern was obtained and confirms the crystalline nature of potassium aluminium silicate [K(AlSi3O8)], sodium silicate (Na2Si2O5), and silicon dioxide (SiO2). FTIR confirms that intense peaks at 445, 795, and 1036 cm−1 are characteristic of Si–O–Si stretching vibration. TEM micrograph of silica nanoparticles found a spherical morphology with an average size of 42 nm. In vitro anti-WSSV (white spot syndrome virus) activity was carried out using PmLyo-Sf9 cells by attachment inhibitory and virucidal activity; the optimum concentration was determined as 320 μg/mL. The interaction of silica nanoparticles and VP28 envelope protein was confirmed using in silico approach. The complexes K(AlSi3O8)-VP28, Na2Si2O5-VP28, and SiO2-VP28 had binding affinities of −5.2, −7.2, and −8.3 Kcal/mol, respectively. [ABSTRACT FROM AUTHOR]

Zika virus infection is a mosquito-borne viral disease that has become a global health concern recently. Zika virus belongs to the Flavivirus genus and is primarily transmitted by Aedes mosquitoes. Prevention of Zika virus infection involves avoiding mosquito bites by using repellent, wearing protective clothing, and staying in screened areas, especially for pregnant women. Treatment focuses on managing symptoms with rest, fluids, and acetaminophen, with close monitoring for pregnant women. Currently, there is no specific antiviral treatment or vaccine for the Zika virus, highlighting the importance of prevention strategies to control its spread. Therefore, in this study, the Zika virus non-structural protein NS3 was targeted to inhibit Zika infection by identifying the novel inhibitor through an in silico approach. Here, 2864 natural compounds were screened using a machine learning-based QSAR model, and later docking was performed to select the potential target. Subsequently, Tanimoto similarity and clustering were performed to obtain the potential target. The three most potential compounds were obtained: (a) 5297, (b) 432449, and (c) 85137543. The protein–ligand complex's stability and flexibility were then investigated by dynamic modelling. The 300 ns simulation showed that 5297 exhibited the steadiest deviation and constant creation of hydrogen bonds. Compared to the other compounds, 5297 demonstrated a superior binding free energy (ΔG = −20.81 kcal/mol) with the protein when the MM/GBSA technique was used. The study determined that 5297 showed significant therapeutic potential and justifies further experimental investigation as a possible inhibitor of the NS2B-NS3 protease target implicated in Zika virus infection. [ABSTRACT FROM AUTHOR]

Autophagy is a new window of science that has been noticed due to the importance of specific therapies in cancer. In this study, the effect of lactoferrin (Lf) on the expression level of ATG101, mTOR and AMPK genes in breast cancer cell line MCF7, as well as the interaction between lactoferrin protein and their protein were investigated. The expression level of the genes was measured using a real-time PCR method. PDB, UniProt, KEGG, and STRING databases and ClusPro webserver and PyMol software were used in silico study. The results showed that the expression level of the ATG101 gene in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.05, 0.13, 0.54 and 0.77, respectively. The expression level of the mTOR gene in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.07, 0.05, 0.13, and 0.49 times respectively. The level of the AMPK gene expression in treatment with concentrations of 100, 400, 600, and 800 μg/ml Lf decreased by 0.05, 0.01, 0.06, and 0.03, respectively. Virtualization of the interaction of Lf protein with ATG101, mTOR and AMPK proteins by Pymol software showed that the N lobe region of Lf interacted with the HORMA domain of ATG101 protein, the fat domain of mTOR protein, and the CTD domain of AMPK protein. Although Lf was not able to increase the expression of autophagy-inducing genes, it may be able to induce autophagy through protein interaction by activating or inhibiting proteins related to autophagy regulation. • The autophagy regulation mechanism of lactoferrin is important in inhibiting cancer cells. • Lactoferrin can be used as a food and drug supplement for the prevention all cancers. • The study of interaction networks of proteins and genes is effective in drug design. • Docking studies have been developed to find unknown biological interactions that occur in the cell. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are cardinal players in numerous physiological and pathological processes. CircRNAs play dual roles as tumor suppressors and oncogenes in different oncological contexts, including hepatocellular carcinoma (HCC). Their roles significantly impact the disease at all stages, including initiation, development, progression, invasion, and metastasis, in addition to the response to treatment. In this review, we discuss the biogenesis and regulatory functional roles of circRNAs, as well as circRNA–protein–mRNA ternary complex formation, elucidating the intricate pathways tuned by circRNAs to modulate gene expression and cellular processes through a comprehensive literature search, in silico search, and bioinformatics analysis. With a particular focus on the interplay between circRNAs, epigenetics, and HCC pathology, the article sets the stage for further exploration of circRNAs as novel investigational theranostic agents in the dynamic realm of HCC. [ABSTRACT FROM AUTHOR]

Context: Diabetes mellitus (DM) is a metabolic disorder disease that causes hyperglycemia conditions and associated with various chronic complications leading to mortality. Due to high toxicity of conventional diabetic drugs, the exploration of natural compounds as alternative diabetes treatments has been widely carried out. Previous in silico studies have highlighted berberine, a natural compound, as a promising alternative in antidiabetic therapy, potentially acting through various pathways, including the inhibition of the FOXO1 transcription factor in the gluconeogenesis pathway. However, the specific mechanism by which berberine interacts with FOXO1 remains unclear, and research in this area is relatively limited. Therefore, this study aims to determine the stability of berberine structure with FOXO1 based on RMSD, RMSF, binding energy, and trajectory analysis to determine the potential of berberine to inhibit the gluconeogenesis pathway. This research was conducted by in silico method with molecular docking using AutoDock4.2 and molecular dynamics study using Amber20, then visualized by VMD. Methods: Docking between ligand and FOXO1 receptor was carried out with Autodock4.2. For molecular dynamics simulations, the force fields of DNA.OL15, protein.ff14SB, gaff2, and tip3p were used. [ABSTRACT FROM AUTHOR]

This intriguing study aimed to explore the reactivity and structural investigation of (3R,3′R)-2,2′,3,3′-tetrahydroneoprzewaquinone A (THNPQ A) as a potential anti-inflammatory agent. Substantially, the electronic properties were investigated using LanL2DZ, 6-311++G (d,p), and STO-3G basis sets, with electronegativity values of 7.9816, 6.3038, and 5.0166 eV, respectively. The natural bond orbital (NBO) analysis calculations of optimization energies revealed that LanL2DZ had the highest stabilization energy (526.65 kcal/mol) for the interaction between πC8-C9 and πC3-C4. Regarding nonlinear optical (NLO) properties, 6-311++G (d,p) exhibited the highest averaged polarizability and first-order hyperpolarizability values, while the polarizability anisotropies Δtotal followed the order 6-311++G (d,p) (65.2054 a.u.) > LanL2DZ (42.8782 a.u.) > STO-3G (29.9349 a.u.). Analysis of the density of states (DOS) and orbital contribution showed that 6-311++G (d,p) had the highest density peaks at both the highest occupied molecular orbital (HOMO) (–0.5 a.u.) and the lowest unoccupied molecular orbital (LUMO) (0.00 a.u.). The condensed dual descriptors indicated minimal variations in the fA– and fA+ values, with an increase in ΔfA, fA–, and fA+ values following the order STO-3G > LanL2DZ > 6-311++G (d,p). The sites for potential nucleophilic attack were identified as O11, O12, O36, and O37, which exhibited the highest values with the STO-3G basis set. Empirical evidence from in vitro inhibition assays unequivocally validates the potent anti-inflammatory activity of THNPQ A. Particularly noteworthy is its exceptional binding affinity, surpassing that of diclofenac. By establishing conventional hydrogen bonds with the glycine of COX-I and histidine of COX-II, THNPQ A exhibits remarkable potential as an effective agent for combating inflammation. These findings boldly emphasize the promising therapeutic prospects of THNPQ A in the field of anti-inflammatory treatment, positioning it as a compelling candidate for further investigation and development. [ABSTRACT FROM AUTHOR]

Nanoparticles exhibit distinct physical and chemical characteristics and are becoming increasingly significant in the production of innovative nanodevices for many applications in physics, biology, biomedicine, and pharmaceuticals. The aim of this research work is to synthesize Fe (II) and Cu (II) nano-sized complexes of trimethoprim (TMP) using the sonication method, characterize them using physical and spectroscopic methods, and carry out ADMET studies on the synthesized complexes. The spectroscopic and physical studies showed a change in colour and an increase in melting point due to coordination. The novel compounds were slightly soluble in water. The XRD tests revealed that the new nanocomplexes were crystalline. The Fe (II) nanocomplexes had a size of 57.56 nm and the Cu (II) nanocomplexes had a size of 69.88 nm. These values were found using Debye-Scherrer’s equation. The FTIR results of the TMP, Fe (II), and Cu (II) nanometal complexes showed a shift of the amino group band from 3317 to 3295 and 3202 cm−1 and the azomethine band from 1633 to 1625 and 1592 cm−1 in the complexes. In the complexes, the proton NMR spectra revealed an upfield shift of the amine proton. The carbon-13 NMR spectra showed that CH2 was involved in coordination with the metal ions. The spectra studies indicated that TMP coordinated with the metal ions through the methylene and amino groups. A trigonal bipyramid structure was proposed for the complexes. The results of the Rule of 5 studies indicated that the test compounds had a good drug-likeness prediction, with only one violation. The ADMET prediction showed that all of the compounds demonstrated improved pharmacokinetic characteristics and adhered to the RO5 requirement. These findings highlight the therapeutic potential of Fe (II) and Cu (II) nano-sized TMP complexes as bioactive compounds that warrant further investigation for pharmaceutical applications. [ABSTRACT FROM AUTHOR]

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Objectives/Background; Several plants with various chemical constituents have been widely explored for managing diabetes mellitus. One of the most common strategies is the inhibitors of the α-amylase and α-glucosidase, key regulatory enzymes in diabetes. This study aims to investigate the anti-diabetic activity of methanolic extract of Coccinia barteri leaves using in vitro α-amylase enzyme inhibition assay and in silico molecular docking study. Methods; The dried pulverized leaf of Coccinia barteri was extracted by maceration using methanol. Qualitative and quantitative phytochemical analyses of the powdered leaf extract were carried out using standard procedures. The extract was fractionated using n-hexane, ethyl acetate, n-butanol and aqueous methanol. In vitro anti-diabetic study of the different fractions and sub-fractions was investigated by α-Amylase Inhibition Assay. Sub-fractions of the ethyl acetate fraction of C.barteri leaf with the highest in vitro anti-diabetic activity were subjected to GC-MS analysis. The compounds detected by GC-MS were selected as ligands for α-amylase and α-glucosidase in the molecular docking study. Results; The phytochemical analysis revealed the presence of saponins, alkaloids, tannins, glycosides, steroids, flavonoids, and cyanide. Compared to the control drug, the ethyl acetate fraction of Coccinia barteri leaf gave a 2-fold lower IC50. GCMS chromatogram of the most active sub-fraction revealed the presence of 18 major compounds. Piperine showed good binding affinity (−6.9 kcal/mol) to α-amylase and displayed hydrogen bonding with ARG 344 and HIS 210, along with pi alkyl bonds with TRP 83, HIS 80, LEU 166, and LEU 232. For α-glucosidase, piperine and 2,4-di-tertbutylphenol surpassed the standard with binding energies of −7.1 kcal/mol and - 6.9 kcal/mol, respectively. Drug likeness and toxicity assessments confirmed adherence to Lipinski's rule, with both compounds showing non-mutagenic and non-tumorigenic properties. Conclusion; The ethyl acetate fraction of the Coccinia barteri leaf exhibits potential anti-diabetic activity, which may be attributed to the inhibition of α-amylase and α-glucosidase, by its constituents, piperine and 2,4-di-tertbutylphenol. [ABSTRACT FROM AUTHOR]

Objective: Aruncus dioicus has been known by the scientific literature and folk experiences for its diverse biological activities, including anti-hyperglycemic effects. Methodology: The aerial parts of the plant collected from Quan Lan Island (Vietnam) were subjected to a methodical theory-experiment investigation for its chemical composition and biological potentials. Results: Firstly, experimental isolation and spectroscopic characterization identified the compositional compounds, ie sambunigrin (1), prunasin (2), uridine (3), and adenosine (4). Secondly, their elucidated structures were predicted with promising bio-chemo-pharmacological potentiality by different computational platforms, ie: docking simulation (docking scores < 10 kcal.mol−1); quantum calculation (dipole moments < 3 Debye); QSARIS model (satisfying Lipinski's rule of five); SwissADME model (satisfying Pires’ interpretations). Finally, the compounds (1-4) were under accumulative purification and in vitro tests against diabetes-related enzymes, ie: protein tyrosine phosphatase 1B (1 with lowest IC50 value 0.39 ± 0.26 μM, 2 with no activity) and α-glucosidase (1 with lowest IC50 value 44.89 ± 0.93 μM, 2 with no activity); also, the inhibitory kinetics based on Lineweaver-Burk and Dixon plot experiments revealed the competitive inhibition mode of 1 against PTP1B (Ki value 0.49 μM). Conclusions: Altogether, the results obtained suggest that A. dioicus and its bioactive compounds, especially sambunigrin (1), uridine (3), and adenosine (4), could be considered as a natural source for further research and development of anti-diabetic agents. [ABSTRACT FROM AUTHOR]

Cleistocalyx operculatus is ubiquitous and known by folk experiences for its antimicrobial properties, thus promising as a low-cost green pesticide. In this work, the plant ethanol extract was investigated against Cercospora nicotianae, a pathogenic fungus implicated in the leaf spot in Pennywort. Characterisation of the plant extract showed 21 identifiable constituents (1-21), with the major components: 4',5'-dimethoxy-2'-hydroxy-4-methylchalcone (21; 41.71 %), phytol (15; 8.46 %), and 5.7-dimethoxyflavanone (20; 5.20 %). The in vitro antifungal screening of the extract revealed potent inhibitory capacity up to 7 days after inoculation (concentration = 9.54 mg.mL-1). The inhibitory potential was predicted by docking simulation, i.e., 19-Q6DQW3 (DS -10.7 kcal.mol-1; DSmax -12.7 kcal.mol-1) > 21-Q6DQW3 (DS -10.3 kcal.mol-1; DSmax -11.9 kcal.mol-1) > 20-Q6DQW3 (DS -10.3 kcal.mol-1 ; DSmax -11.7 kcal.mol-1). The chemical potentiality was derived from quantum calculation, i.e., 22 (-1172.77 a.u.) > 21 ≈ 19 (approx. - 1000 a.u.) > 20 (-ca. -950 a.u.) for chemical stability, and 3 (3.40 Debye), 15 (2.47 Debye), and 5 (2.03 Debye) for physical compatibility. The suitability for biological and pesticidal applications was justified by physicochemical analyses. The results revealed a firm correlation between the extracted major constituents (20 and 21) and the total antifungal activity against C. nicotianae, thus encouraging its local usage. [ABSTRACT FROM AUTHOR]

Botanicals contain complex mixtures of chemicals most of which lack pharmacokinetic data in humans. Since physicochemical and pharmacokinetic properties dictate the in vivo exposure of botanical constituents, these parameters greatly impact the pharmacological and toxicological effects of botanicals in consumer products. This study sought to use computational (i.e., in silico) models, including quantitative structure–activity relationships (QSAR) and physiologically based pharmacokinetic (PBPK) modeling, to predict properties of botanical constituents. One hundred and three major constituents (e.g., withanolides, mitragynine, and yohimbine) in 13 botanicals (e.g., ashwagandha, kratom, and yohimbe) were investigated. The predicted properties included biopharmaceutical classification system (BCS) classes based on aqueous solubility and permeability, oral absorption, liver microsomal clearance, oral bioavailability, and others. Over half of these constituents fell into BCS classes I and II at dose levels no greater than 100 mg per day, indicating high permeability and absorption (%Fa > 75%) in the gastrointestinal tract. However, some constituents such as glycosides in ashwagandha and Asian ginseng showed low bioavailability after oral administration due to poor absorption (BCS classes III and IV, %Fa < 40%). These in silico results fill data gaps for botanical constituents and could guide future safety studies. For example, the predicted human plasma concentrations may help select concentrations for in vitro toxicity testing. Additionally, the in silico data could be used in tiered or batteries of assays to assess the safety of botanical products. For example, highly absorbed botanical constituents indicate potential high exposure in the body, which could lead to toxic effects. Botanicals contain complex mixtures of chemicals most of which lack pharmacokinetic data in humans. This study used computational models, including quantitative structure–activity relationships (QSAR) and physiologically based pharmacokinetic (PBPK) modeling, to predict properties of 103 botanical constituents in 13 botanicals. Over half constituents had high permeability and absorption at oral doses no greater than 100 mg per day. However, most glycosides showed low bioavailability after oral administration due to low absorption. [ABSTRACT FROM AUTHOR]

Metabolomics, the study of small-molecule metabolites within biological systems, has become a potent instrument for understanding cellular processes. Despite its profound insights into health, disease, and drug development, identifying the protein partners for metabolites, especially dietary phytochemicals, remains challenging. In the present study, we introduced an innovative in silico, structure-based target prediction approach to efficiently predict protein targets for metabolites. We analyzed 27 blood serum metabolites from nutrition intervention studies' blueberry-rich diets, known for their health benefits, yet with elusive mechanisms of action. Our findings reveal that blueberry-derived metabolites predominantly interact with Carbonic Anhydrase (CA) family proteins, which are crucial in acid-base regulation, respiration, fluid balance, bone metabolism, neurotransmission, and specific aspects of cellular metabolism. Molecular docking showed that these metabolites bind to a common pocket on CA proteins, with binding energies ranging from −5.0 kcal/mol to −9.0 kcal/mol. Further molecular dynamics (MD) simulations confirmed the stable binding of metabolites near the Zn binding site, consistent with known compound interactions. These results highlight the potential health benefits of blueberry metabolites through interaction with CA proteins. [ABSTRACT FROM AUTHOR]

The pathological manifestation of the inflammatory process primarily stems from the heightened release of pro-inflammatory cytokines, with IL-1β standing out as a pivotal cytokine. The excessive presence of IL-1β disrupts immune signaling, thereby assuming a pathogenic and exacerbating role in the pathophysiology of numerous inflammatory diseases. Regulating IL-1β levels becomes crucial, and the IL-1Ra molecule serves this purpose by binding to the IL-1R1 receptor, thereby impeding the binding of IL-1β. Several pharmaceuticals have entered the market, aiming to neutralize IL-1β's biological function through diverse mechanisms. However, the existing IL-1β inhibitors are recombinant proteins, characterized by a high production cost and limited stability. Therefore, this study aimed to predict a peptide, named DAP1-2, based on the IL-1Ra molecule. DAP1-2 was designed to attenuate responses triggered by IL-1β by blocking the IL-1R1 receptor. The selection of amino acids from the IL-1Ra molecule (PDB: I1RA) that interact with the three domains of the IL-1R1 receptor was performed using Swiss PDB Viewer. After prediction, chemical synthesis was made using the Fmoc-Synthesis technique. The efficacy of DAP1-2 was assessed using RAW 264.7 cells, which were exposed to LPS (5 μg/mL) for 24 h to induce IL-1β expression and treated with the peptides in different concentrations. IL-1β levels were assessed using ELISA, and the gene expression of IL-1β was measured by RT-qPCR, additionally to the viability test. Results revealed a significant reduction in IL-1β levels and gene expression in cells stimulated by LPS and treated with DAP1-2 in different concentrations. Furthermore, the MTT assay confirmed the nontoxic nature of the peptides on the cell lineage. This alternative approach shows promise as an IL-1 inhibitor, due to the stability, ease of production, and cost-effectiveness provided by the use of synthetic peptides. [ABSTRACT FROM AUTHOR]

The environmental contamination by extremophile Aspergillus species, i.e., Aflatoxin B1, is hardly controllable in Southeast Asia and Sub-Saharan Africa, which lack handling resources and controlled storage facilities. Acute aflatoxicosis poisoning from aflatoxin-prone dietary staples could cause acute hepatic necrosis, acute liver failure, and death. Here, as the cheaper, more straightforward, and facile on-site diagnostic kit is needed, we report an ultraviolet-excitable optical aptasensor based on a fluorinated ethylene propylene film strip. Molecular dynamics on the aptamer.AFB1 complex revealed that the AFB1 to the aptamer increases the overall structural stability, suggesting that the aptamer design is suitable for the intended application. Under various influencing factors, the proposed label-free strategy offers a fast 20-min on-site fabrication simplicity and 19-day shelf-life. The one-pot incubation provides an alternative to catalytic detection and exhibited 4 times reusability. The recovery of crude brown sugar, processed peanuts, and long-grain rice were 102.74 ± 0.41 (n = 3), 86.90 ± 3.38 (n = 3), and 98.50 ± 0.42 (n = 3), comparable to High-Performance Liquid Chromatography-Photodiode Array Detector results. This study is novel owing to the peculiar UV-active spectrum fingerprint and the convenient use of hydrophobic film strips that could promote breakthrough innovations and new frontiers for on-site/forensic detection of environmental pollutants. [ABSTRACT FROM AUTHOR]

Objectives: Chagas Disease, caused by the parasite Trypanosoma cruzi, remains a significant public health concern, particularly in Latin America. The current standard treatment for Chagas Disease, benznidazole, is associated with various side effects, necessitating the search for alternative therapeutic options. In this study, we aimed to identify potential therapeutics for Chagas Disease through a comprehensive computational analysis. Methods: A library of compounds derived from Cananga odorata was screened using a combination of pharmacophore modeling, structure-based screening, and quantitative structure-activity relationship (QSAR) analysis. The pharmacophore model facilitated the efficient screening of the compound library, while the structure-based screening identified hit compounds with promising inhibitory potential against the target enzyme, sterol-14-alpha demethylase. Results: The QSAR model predicted the bioactivity of the hit compounds, revealing one compound to exhibit superior activity compared to benznidazole. Evaluation of the physicochemical, pharmacokinetic, toxicity, and medicinal chemistry properties of the hit compounds indicated their drug-like characteristics, oral bioavailability, ease of synthesis, and reduced toxicity profiles. Conclusion: Overall, our findings present a promising avenue for the discovery of novel therapeutics for Chagas Disease. The identified hit compounds possess favorable drug-like properties and demonstrate potent inhibitory effects against the target enzyme. Further in vitro and in vivo studies are warranted to validate their efficacy and safety profiles. [ABSTRACT FROM AUTHOR]

AbstractNano-metal technology has emerged recently as an exceptional biological targeted field with numerous advantages like small size and high surface charge. In this report, we described our research on the stabilization of prepared silver nanocores coated with bovine serum albumin and further loaded with methotrexate (MTX) drug. The prepared nanoparticles were characterized by using UV-Visible, X-ray diffraction (XRD), energy dispersive X-ray (EDX), scanning electron microscopy (SEM) and cyclic voltammetry (CV). The UV spectra of AgNP showed a prominent peak at 400 nm. The presence of MTX was confirmed by the FT-IR and EDX analysis. The AgNP-BSA-MTX particles resembled elliptical shape like structures in the SEM images. In-vitro drug release for free drug MTX occurred rapidly in a period of 12 hrs (85%), whereas a sustained release of MTX greater than 85% from the AgNP-BSA-MTX nanoparticles was observed for 48 hrs. The AgNP-BSA-MTX demonstrated a five-fold higher cytotoxic activity compared to free MTX drug alone against PC-3 cell lines, performed by the 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay method. DNA binding studies were performed for the AgNP-BSA-MTX with calf thymus DNA (ct-DNA). In-silico studies were performed for MTX with DNA (Protein Data Bank ID-IZ3F) and a prominent interaction with the nucleotides was noted. Molecular Dynamics (MD) simulation studies were also performed for the docked MTX-DNA complex. The average of the Root mean square deviation (RMSD) values for the DNA backbone was calculated to be 5.71 ± 0.48 nm. [ABSTRACT FROM AUTHOR]

Canine distemper virus (CDV) affects many domestic and wild animals. Variations among CDV genome linages could lead to vaccination failure. To date, there are several vaccine alternatives, such as a modified live virus and a recombinant vaccine; however, most of these alternatives are based on the ancestral strain Onderstepoort, which has not been circulating for years. Vaccine failures and the need to update vaccines have been widely discussed, and the development of new vaccine candidates is necessary to reduce circulation and mortality. Current vaccination alternatives cannot be used in wildlife animals due to the lack of safety data for most of the species, in addition to the insufficient immune response against circulating strains worldwide in domestic species. Computational tools, including peptide-based therapies, have become essential for developing new-generation vaccines for diverse models. In this work, a peptide-based vaccine candidate with a peptide library derived from CDV H and F protein consensus sequences was constructed employing computational tools. The molecular docking and dynamics of the selected peptides with canine MHC-I and MHC-II and with TLR-2 and TLR-4 were evaluated. In silico safety was assayed through determination of antigenicity, allergenicity, toxicity potential, and homologous canine peptides. Additionally, in vitro safety was also evaluated through cytotoxicity in cell lines and canine peripheral blood mononuclear cells (cPBMCs) and through a hemolysis potential assay using canine red blood cells. A multiepitope CDV polypeptide was constructed, synthetized, and evaluated in silico and in vitro by employing the most promising peptides for comparison with single CDV immunogenic peptides. Our findings suggest that predicting immunogenic CDV peptides derived from most antigenic CDV proteins could aid in the development of new vaccine candidates, such as multiple single CDV peptides and multiepitope CDV polypeptides, that are safe in vitro and optimized in silico. In vivo studies are being conducted to validate potential vaccines that may be effective in preventing CDV infection in domestic and wild animals. [ABSTRACT FROM AUTHOR]

The use of Latin origin terms, relevant for sample characterization modalities, is described with a focus on samples under controlled conditions, samples within devices, and samples during physico-chemical evolution. The terms in vitro, in vivo, in situ, ab initio, in silico, post mortem, ex situ, posthumous, in vacuo, (in) operando, post facto, and ex post facto, as used in the scientific literature, are considered. Uses of the Latin origin terms in situ, extra situm, in operando, in vivo, in vacuo, in vitro, extra vivum, post facto and ex post facto, ab initiis, computatro, and post mortem are discussed. It is suggested that these terms are to be used without hyphenation and that all Latin derived terms are set in italic font. [ABSTRACT FROM AUTHOR]

Marburg virus (MARV) is a highly contagious and virulent agent belonging to Filoviridae family. MARV causes severe hemorrhagic fever in humans and non-human primates. Owing to its highly virulent nature, preventive approaches are promising for its control. There is currently no approved drug or vaccine against MARV, and management mainly involves supportive care to treat symptoms and prevent complications. Our aim was to design a novel multi-epitope vaccine (MEV) against MARV using immunoinformatics studies. In this study, various proteins (VP35, VP40 and glycoprotein precursor) were used and potential epitopes were selected. CTL and HTL epitopes covered 79.44% and 70.55% of the global population, respectively. The designed MEV construct was stable and expressed in Escherichia coli (E. coli) host. The physicochemical properties were also acceptable. MARV MEV candidate could predict comprehensive immune responses such as those of humoral and cellular in silico. Additionally, efficient interaction to toll-like receptor 3 (TLR3) and its agonist (β-defensin) was predicted. There is a need for validation of these results using further in vitro and in vivo studies. [ABSTRACT FROM AUTHOR]

Background: This study investigates the relative expression of the Na+, HCO3- cotransport gene NBCn1, and caspase-3 within the tumor microenvironment of human breast cancer, considering the in vivo microenvironment. Method: In this experimental study, breast cancer MDA-MB-231 cells were cultured under normoxia/hypoxia conditions for 24, 48, and 72 hours with varying glucose concentrations (5.5, 11, and 25 mM). The mRNA expression of NBCn1 and caspase-3 was evaluated using real-time polymerase chain reaction. The stability and binding pocket of NBCn1 were assessed using DispHred and the Computed Atlas of Surface Topography of proteins (CASTp) servers, respectively. The location prediction of the protein was determined using the Transmembrane Helices; Hidden Markov Model (TMHMM) server. Results: Normoxia led to an increase in NBCn1 expression during all three time periods, displaying heterogeneity. The expression was particularly elevated at glucose concentrations of 25 and 5.5 mM. In hypoxic conditions, gene expression was reduced; however, an increase in glucose concentration enhanced SLC4A7 expression. Specifically, a glucose concentration of 25 mM led to decreased caspase-3 expression under hypoxic conditions. In silico studies revealed that SLC4A7 becomes disordered when the pH falls below 7, with most amino acids in the binding pocket being nonpolar. Conclusion: The heightened risk of breast cancer metastasis may be linked to the upregulation of SLC4A7 and downregulation of caspase-3 expression, underscoring their fundamental roles in cancer treatment and prevention. SLC4A7 is a transmembrane protein, and its folding is pH-dependent. [ABSTRACT FROM AUTHOR]

The occurrence of antibacterial resistance has become a global concern. The results of previous studies revealed many cases of antibacterial resistance of levofloxacin in H. pylori strains originating from Indonesia. Conventional attempts to obtain new antibacterial agents usually take a long time, other efforts are needed to speed up discovery. Databases that provide the structure of DNA gyrases cannot fully provide what is needed. This study aims to obtain the three-dimensional structure of DNA gyrase of the Indonesian H. pylori strain so that it can be used to simulate the interaction process of compounds that have the potential to be anti-H. pylori through in silico studies. This study used in silico methods to predict the absorption, distribution, metabolism, excretion, and toxicology of potential compounds. The next process involves screening for drug similarity based on criteria set by Muegge, Egan, Veber, Lipinski, and Ghose. The three-dimensional structure of DNA gyrase is formed from several samples of amino acid sequences from the Indonesian gyrA and gyrB H. pylori strains. Eligible potential compounds were subjected to molecular docking studies on gyrA and gyrB to obtain the best score. The three-dimensional structure of the Indonesian gyrA and gyrB H. pylori strains has been obtained. Eugenol, cinnamaldehyde, and ethyl p-methoxycinnamate were more easily absorbed compared to curcumin and levofloxacin as controls. Curcumin and hesperidin show poor absorption and longer distribution in the gastric mucosa, thus allowing long-term interaction with H. pylori. All compounds do not inhibit cytochrome P450, can be excreted by the body, and are non-toxic. The prediction of drug similarity passes only through curcumin and ethyl p-methoxycinnamate. The results of molecular docking concluded that curcumin and hesperidin had better scores than levofloxacin. Curcumin has the most potential as an anti-H. pylori. [ABSTRACT FROM AUTHOR]

Spirulina platensis with bioactive compounds such as Phycocyanin, β-carotene, Genistein and α-glucan, have been shown to have anti-inflammatory properties. Our present study investigation utilizes an in silico methodology to examine the molecular interactions between Spirulina platensis chemicals compound with TNFa and p21. Utilizing computational techniques molecular docking, our goal is to clarify the possible pathways by which Spirulina platensis chemicals could affect these important regulators and postpone cellular senescence. Our research may shed important light on the creation of Spirulina platensis-based therapies for ageing and age-related illnesses. Our results imply that Spirulina platensis may contribute to overall cellular health and the mitigation of cellular senescence. Phycocyanin has the most negative ΔG value is -15.0 kcal/mol. Genistein has the lowest Ki value, namely 7.299 μM. The ΔG and Ki values of Genistein were lower than Quercetin. The potential chemical interactions between substances generated from Spirulina platensis and senescence pathways, including those involving TNFa and p21, are highly intriguing for the development of innovative therapeutic approaches targeted at ameliorating cellular senescence dysfunction associated with aging. [ABSTRACT FROM AUTHOR]

This study aims to explore the relationship between 4-Hydroxycinnamic Acid, a compound found in broccoli fruit (Brassica oleracea var. italica), and Estrogen Receptor Beta Protein through in silico analysis. The research was conducted using Pymol, MOE 2015, Discovery Studio 2016, and Lepinski Rule software. These tools were employed to model the structure of both the compound and protein, as well as to evaluate their interaction. The results revealed a significant interaction with a Binding Affinity of -6.4182. Moreover, the Root Mean Square Deviation (RMSD) measurements yielded a value of 3.8907, indicating the degree of agreement between the compound and protein structures. Analysis using the Lepinski Rule disclosed the characteristics of the compound 4-Hydroxycinnamic Acid, including a mass of 164, two hydrogen bond donors, three hydrogen bond acceptors, a log P value of 1.490, and a molar reactivity of 44.776. These findings provide valuable insights into the potential of 4-Hydroxycinnamic Acid in interacting with Estrogen Receptor Beta Protein, which could serve as a foundation for further research on the health benefits and therapeutic applications of this compound, contributing to the goal of good health and well-being. [ABSTRACT FROM AUTHOR]

Gene expression alterations in postmortem schizophrenia tissue are well-documented and are influenced by genetic, medication, and epigenetic factors. The Wingless/Integrated (WNT) signaling pathway, critical for cell growth and development, is involved in various cellular processes including neurodevelopment and synaptic plasticity. Despite its importance, WNT signaling remains understudied in schizophrenia, a disorder characterized by metabolic and bioenergetic defects in cortical regions. In this study, we examined the gene expression of 10 key WNT signaling pathway transcripts: IQGAP1, CTNNβ1, GSK3β, FOXO1, LRP6, MGEA5, TCF4, βTRC, PPP1Cβ, and DVL2 in the dorsolateral prefrontal cortex (DLPFC) using postmortem tissue from schizophrenia subjects (n = 20, 10 males, 10 females) compared to age, pH, and postmortem interval (PMI)-matched controls (n = 20, 10 males, 10 females). Employing the R-shiny application Kaleidoscope, we conducted in silico "lookup" studies from published transcriptomic datasets to examine cell- and region-level expression of these WNT genes. In addition, we investigated the impact of antipsychotics on the mRNA expression of the WNT genes of interest in rodent brain transcriptomic datasets. Our findings revealed no significant changes in region-level WNT transcript expression; however, analyses of previously published cell-level datasets indicated alterations in WNT transcript expression and antipsychotic-specific modulation of certain genes. These results suggest that WNT signaling transcripts may be variably expressed at the cellular level and influenced by antipsychotic treatment, providing novel insights into the role of WNT signaling in the pathophysiology of schizophrenia. [ABSTRACT FROM AUTHOR]

Liver cancer is a worldwide issue that also affects the Malaysian population. The occurrence is closely related to risk factors like chronic infections and environmental exposures. Due to the toxicity of conventional therapeutic drugs for liver cancer, bioactive peptides have emerged as a popular alternative anticancer agent. Although the full-length pardaxin from Pardachirus marmoratus was proven with anticancer effects, its concurrent haemolytic effects are yet to be resolved. Therefore, this study utilized in silico and in vitro analyses to assess cytotoxic effects induced by the shortened pardaxin derivatives. The in silico findings led to the discovery of a series of shortened pardaxin derivatives with 13 amino acids, where single residue replacement prediction by bioinformatics tools was done on the shortened sequences. Among the top five shortened derivatives, the derivative where amino acid threonine was replaced by proline, was identified as the most potential candidate, namely LL13. The LL13 peptide was predicted with improved anticancer effects, non-toxic, and alleviated haemolytic effects as compared to its parental peptide. The subsequent cytotoxicity testing further validated its selective toxicity against liver cancer cells, HepG2 cells, with relatively lower killing effects on the normal cells, Vero cells. These in vitro findings validated the in silico predictions and also indicated that this peptide has potential as an anticancer drug with selective targeting capabilities. In conclusion, this study has highlighted the potential of using a combination of in silico and in vitro approaches to discover potentially shortened peptides as a novel therapeutic option for liver cancer treatment. [ABSTRACT FROM AUTHOR]

Statins are cholesterol-lowering drugs with a mechanism of inhibiting 3-hydroxy-3- methylglutaryl-CoA reductase, but long-term use can cause side effects. An example of a plant capable of reducing cholesterol levels is Angelica keiskei (ashitaba). Therefore, this study aimed to obtain suitable compounds with inhibitory activity against the HMG-CoA reductase enzyme from ashitaba through in silico tests. The experiment began with screening and pharmacophore modeling, followed by molecular docking on ashitaba’s compounds, statins groups, and the native ligand was (3R,5R)-7-[4-(benzyl carbamoyl)-2-(4-fluorophenyl)-5-(1-methylethyl)-1H-imidazole1-yl]-3,5-dihydroxyheptanoic acid (4HI). Based on the results of the molecular docking simulations, 15 hit compounds had a small binding energy (∆G). Pitavastatin, as the comparator drug (∆G = −8.24 kcal/mol; Ki = 2.11 µM), had a lower ∆G and inhibition constant (Ki) than the native ligand 4HI (∆G = −7.84 kcal/mol; Ki = 7.96µM). From ashitaba’s compounds, it was found that 4′ -O-geranylnaringenin, luteolin, isobavachalcone, dorsmannin A, and 3′ -carboxymethyl-4,2′ - dihydroxy-4′ -methoxychalcone have low ∆G of below −6 kcal/mol. The lowest ∆G value was found in 3′ -carboxymethyl-4,2′ -dihydroxy-4′ -methoxy chalcone with a ∆G of −6.67 kcal/mol and Ki value of 16.66 µM, which was lower than the ∆G value of the other comparator drugs, atorvastatin (∆G = −5.49 kcal/mol; Ki = 1148.17 µM) and simvastatin (∆G = −6.50 kcal/mol; Ki = 22.34 µM). This compound also binds to the important amino acid residues, including ASN755D, ASP690C, GLU559D, LYS735D, LYS691C, and SER684C, through hydrogen bonds. Based on the results, the compound effectively binds to six important amino acids with good binding affinity and only requires a small concentration to reduce half of the enzyme activity [ABSTRACT FROM AUTHOR]

Simple Summary: The black cutworm, Agrotis ipsilon (Hufnagel), poses a significant threat to various crops. Marjoram (Origanum majorana) and rosemary (Rosmarinus officinalis) essential oils (EOs) were investigated for their toxicity using in vitro and in silico methods. GC-MS analysis identified the main constituents, with O. majorana being more toxic than R. officinalis to A. ipsilon larvae. R. officinalis EO inhibited Na+/K+ pump activity consistently, while O. majorana showed varied effects. Both EOs influenced detoxification enzymes differently over time. Molecular docking indicated a strong binding affinity of the main EO constituents to target enzymes. These findings suggest the potential of EOs as insecticides in integrated pest management programs, particularly in organic agriculture. In this study, in vitro and in silico approaches were employed to assess the toxicity of marjoram (Origanum majorana) and rosemary (Rosmarinus officinalis) essential oils (EOs) to A. ipsilon larvae. The study determined the activities of ATPases in the larvae after treatment with the LC20 and LC70 of each EO. α-esterase and glutathione-S-transferase (GST) activities were also determined after treatment with LC10 and LC30 of each EO. Furthermore, molecular docking was employed to determine the binding affinity of terpinene-4-ol and α-pinene, the major constituents of O. majorana, and R. officinalis EOs, respectively, compared to the co-crystallized ligand of α-esterase, diethyl hydrogen phosphate (DPF). Toxicity assays revealed that O. majorana EO was more toxic than R. officinalis EO to the A. ipsilon larvae at 96 h post-treatment. However, the LC20 and LC70 of the latter significantly inhibited the activity of the Na+-K+ pump at almost all intervals. The same concentrations significantly inhibited the Mg2+/Ca2+-ATPase and Ca2+ pump at 96 h post-treatment. In contrast, O. majorana EO showed a variable effect on the Na+-K+ pump across different time intervals. On the other hand, LC10 and LC30 of both EOs showed varied effects on α-esterase and GST over time. Molecular docking revealed energy scores of −4.51 and −4.29 kcal/mol for terpinene-4-ol and α-pinene, respectively, compared to a score of −4.67 for PDF. Our study demonstrated the toxicity of the tested EOs to A. ipsilon, suggesting their potential efficacy as insecticides. [ABSTRACT FROM AUTHOR]

In silico modeling offers an opportunity to supplement and accelerate cardiac safety testing. With in silico modeling, computational simulation methods are used to predict electrophysiological interactions and pharmacological effects of novel drugs on critical physiological processes. The O'Hara-Rudy's model was developed to predict the response to different ion channel inhibition levels on cardiac action potential duration (APD) which is known to directly correlate with the QT interval. APD data at 30% 60% and 90% inhibition were derived from the model to delineate possible ventricular arrhythmia scenarios and the marginal contribution of each ion channel to the model. Action potential values were calculated for epicardial, myocardial, and endocardial cells, with action potential curve modeling. This study assessed cardiac ion channel inhibition data combinations to consider when undertaking in silico modeling of proarrhythmic effects as stipulated in the Comprehensive in Vitro Proarrhythmia Assay (CiPA). As expected, our data highlight the importance of the delayed rectifier potassium channel (IKr) as the most impactful channel for APD prolongation. The impact of the transient outward potassium channel (Ito) inhibition on APD was minimal while the inward rectifier (IK1) and slow component of the delayed rectifier potassium channel (IKs) also had limited APD effects. In contrast, the contribution of fast sodium channel (INa) and/or L-type calcium channel (ICa) inhibition resulted in substantial APD alterations supporting the pharmacological relevance of in silico modeling using input from a limited number of cardiac ion channels including IKr, INa, and ICa, at least at an early stage of drug development. [ABSTRACT FROM AUTHOR]

In the early 2000s pharmaceutical drug discovery was beginning to use computational approaches for absorption, distribution, metabolism, excretion and toxicity (ADME/Tox, also known as ADMET) prediction. This emphasis on prediction was an effort to reduce the risk of later stage failures from ADME/Tox. Much has been written in the intervening twenty plus years and significant expenditure has occurred in companies developing these in silico capabilities which can be gleaned from publications. It is therefore an appropriate time to briefly reflect on what was proposed then and what the reality is today. 20 years ago, we tended to optimise bioactivity and perhaps one ADME/Tox property at a time. Previously pharmaceutical companies needed a whole infrastructure for models – in silico and in vitro experts, IT, champions on a project team, educators and management support. Now we are in the age of generative de novo design where bioactivity and many ADME/Tox properties can be optimised and large language model technologies are available. There are also some challenges such as the focus on very large molecules which may be outside of current ADME/Tox models. We provide an opportunity to look forward with the increasing public data for ADME/Tox as well as expanded types of algorithms available. [ABSTRACT FROM AUTHOR]

In this study, we synthesized 15 novel quinazoline‐morpholinobenzylideneamino hybrid compounds from methyl anthranilate and we assessed their cytotoxicity via in vitro assays against A549 and BEAS‐2B cell lines. Molecular docking studies were conducted to evaluate the protein‐ligand interactions and inhibition mechanisms on nine different molecular targets, while molecular dynamics (MD) simulations were carried out to assess the stability of the best docked ligand–protein complexes. Additionally, ADME prediction was carried out to determine physicochemical parameters and drug likeness. According to the cytotoxicity assays, compound 1 (IC50 = 2.83 μM) was found to be the most active inhibitor against A549 cells. While the selectivity index (SI) of compound 1 is 29, the SI of the reference drugs paclitaxel and sorafenib, used in this study, are 2.40 and 4.92, respectively. Among the hybrid compounds, 1 has the best docking scores against VEGFR1 (−11.744 kcal/mol), VEGFR2 (−12.407 kcal/mol) and EGFR (−10.359 kcal/mol). During MD simulations, compound 1 consistently exhibited strong hydrogen bond interactions with the active sites of VEGFR1 and 2, and these interactions were maintained for more than 90% of the simulation time. Additionally, the RMSD and RMSF values of the ligand–protein complexes exhibited high stability at their minimum levels around 1–2 Å. In conclusion, these findings suggest that compound 1 may be a potent and selective inhibitor candidate for lung cancer treatment and inhibition of VEGFR2, especially. [ABSTRACT FROM AUTHOR]

Herein, the synthesis and biological evaluation of 6-fluoro-3-(piperidin-4-yl)benzo[d]isoxazole sulfonamide hybrids are discussed. All the synthesized molecules were assessed for anti-cancer and anti-TB activities using in vitro and in silico methods. The molecular docking study with CDK8 as a possible target for anti-cancer activity demonstrated that compounds 2, 3, 5, 7, 8, and 9 have a good binding affinity ranging from −8.7 to −10.3 kcal/mol against CDK8 (PDB 6T41) protein as compared with the standard drug 5-Fluorouracil (−5.0 kcal/mol). The in vitro anti-mycobacterial screening reveals that compounds 2 and 3 elicited moderate anti-TB activity with a MIC value of 25 µM. Compounds 2 and 3 exhibited moderate in vitro anti-proliferative potency against the cancer cell lines MCF-7 and HCT-116. Moreover, compound 3 exhibited a better anti-oxidant effect among all tested compounds. Some quantum chemical parameters and drug-likeness profiling of the molecules were modeled by density functional theory (DFT) and ADME studies. The obtained theoretical results are in good agreement with the experimental results. [ABSTRACT FROM AUTHOR]

BACKGROUND: Faced with the need to develop new herbicides with modes of action different to those observed for existing agrochemicals, one of the most promising strategies employed by synthetic chemists involves the structural modification of molecules found in natural products. Molecules containing amides, imides, and epoxides as functional groups are prevalent in nature and find extensive application in synthesizing more intricate compounds due to their biological properties. In this context, this paper delineates the synthesis of N‐phenylnorbornenesuccinimide derivatives, conducts biological assays, and carries out in silico investigation of the protein target associated with the most potent compound in plant organisms. The phytotoxic effects of the synthesized compounds (2–29) were evaluated on Allium cepa, Bidens pilosa, Cucumis sativus, Sorghum bicolor, and Solanum lycopersicum. RESULTS: Reaction of endo‐bicyclo[2.2.1]hept‐5‐ene‐3a,7a‐dicarboxylic anhydride (1) with aromatic amines led to the N‐phenylnorbornenesuccinic acids (2–11) with yields ranging from 75% to 90%. Cyclization of compounds (2–11) in the presence of acetic anhydride and sodium acetate afforded N‐phenylnorbornenesuccinimides (12–20) with yields varying from 65% to 89%. Those imides were then subjected to epoxidation reaction to afford N‐phenylepoxynorbornanesuccimides (21–29) with yields from 60% to 90%. All compounds inhibited the growth of seedlings of the plants evaluated. Substance 23 was the most active against the plants tested, inhibiting 100% the growth of all species in all concentrations. Cyclophilin was found to be the enzymatic target of compound 23. CONCLUSION: These findings suggest that derivatives of N‐phenylnorbornenesuccinimide are promising compounds in the quest for more selective and stable agrochemicals. This perspective reinforces the significance of these derivatives as potential innovative herbicides and emphasizes the importance of further exploring their biological activity on weeds. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Aquaporin (AQP) is a water channel protein from the family of transmembrane proteins which facilitates the movement of water across the cell membrane. It is ubiquitous in nature, however the understanding of the water transport mechanism, especially for AQPs in microbes adapted to low temperatures, remains limited. AQP also has been recognized for its ability to be used for water filtration, but knowledge of the biochemical features necessary for its potential applications in industrial processes has been lacking. Therefore, this research was conducted to express, extract, solubilize, purify, and study the functional adaptations of the aquaporin Z family from Pseudomonas sp. AMS3 via molecular approaches. In this study, AqpZ1 AMS3 was successfully subcloned and expressed in E. coli BL21 (DE3) as a recombinant protein. The AqpZ1 AMS3 gene was expressed under optimized conditions and the best optimized condition for the AQP was in 0.5 mM IPTG incubated at 25°C for 20 h induction time. A zwitterionic mild detergent [(3‐cholamidopropyl) dimethylammonio]‐1‐propanesulfonate was the suitable surfactant for the protein solubilization. The protein was then purified via affinity chromatography. Liposome and proteoliposome was reconstituted to determine the particle size using dynamic light scattering. This information obtained from this psychrophilic AQP identified provides new insights into the structural adaptation of this protein at low temperatures and could be useful for low temperature application and molecular engineering purposes in the future. [ABSTRACT FROM AUTHOR]