Five undescribed aryltetralin lignans with cytotoxic activities from the fruits of Cleistanthus eberhardtii.

Five undescribed lignans, cleiseberharnins A-D (1-4), cleiseberharside A (5) were isolated from the fruits of Cleistanthus eberhartii (Phyllanthaceae), together with six known aryltetralin lignans, cleistantoxin (6), picroburseranin (7), neocleistantoxin (8), 7-hydroxypicropolygamain (9), cleisindoside D (10), and cleisindoside A (11). Their structures and relative configurations were established by analysis of HRESIMS and NMR data, and quantum chemical calculations of JH,H coupling constants. The absolute configurations of 1-5 were determined by analysis of their experimental CD spectra and comparison with calculated electronic circular dichroism (ECD) spectra. All compounds (1-11) were evaluated for their cytotoxicity against KB, MCF-7, HepG-2, and Lu-1 human cancer cell lines. Among the tested compounds, compounds 6 and 7 showed strong activity against KB, MCF7, HepG2 and Lu-1 cell lines with IC50 values in the range of 0.02-0.62 µM. Compound 1 showed activity against three cancer cell lines KB, HepG2, and Lu-1 with IC50 values of 6.98, 7.61 and 11.75 µM, respectively. Compound 2 exhibited a selective inhibition with moderate cytotoxicity against Lu-1 with IC50 value of 15.30 µM. Compounds 4, 5 and 9 showed moderate activity against the three cancer cell lines with IC50 values in the range of 8.73-19.70 µM.

Isolation of oleanolic acid from Clematis armandii for differentiation it from adulterants by HPTLC/HPLC.

Clematis armandii has been used in many Chinese traditional patent medicines all over the world as a form of Caulis Clematidis Armandii. However, it has often been adulterated by Aristolochia manshuriensis, and Iodes vitiginea. A. manshuriensis must not be part of any herbal medicines because it contains aristolochic acid I, a nephrotoxin and potential carcinogen. The current pharmacopoeial methods have had limitation for differentiation of C. armandii from its adulterants. Thus, a specific, comprehensive, sensitive, and reproducible HPTLC/HPLC for quality control of C. armandii was proposed. Oleanolic acid from C. armandii has been isolated by vacuum liquid chromatography and column chromatography. The purified compound has been identified using Ultra Violet spectrophotometry (UV-Vis), Fourier Transform Infrared (FTIR), mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. Therefore, oleanolic acid should be detected for positive identification of Caulis Clematis Armandii. Minimum content of oleanolic acid can be evaluated by the validated HPTLC procedure proposed as well.

Targeting Olokizumab-Interleukin 6 interaction interface to discover novel IL-6 inhibitors.

The IL-6/IL-6R or IL-6/GP130 protein-protein interactions play a significant role in controlling the development of chronic inflammatory diseases, such as rheumatoid arthritis, Castleman disease, psoriasis, and, most recently, COVID-19. Modulating or antagonizing protein-protein interactions of IL6 binding to its receptors by oral drugs promises similar efficacy to biological therapy in patients, namely monoclonal antibodies. In this study, we used a crystal structure of the Fab part of olokizumab in a complex with IL-6 (PDB ID: 4CNI) to uncover starting points for small molecule IL-6 antagonist discovery. Firstly, a structure­based pharmacophore model of the protein active site cavity was generated to identify possible candidates, followed by virtual screening with a significant database Drugbank. After the docking protocol validation, a virtual screening by molecular docking was carried out and a total of 11 top hits were reported. Detailed analysis of the best scoring molecules was performed with ADME/T analysis and molecular dynamics simulation. Furthermore, the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) technique has been utilized to evaluate the free binding energy. Based on the finding, one newly obtained compound in this study, namely DB15187, may serve as a lead compound for the discovery of IL-6 inhibitors.Communicated by Ramaswamy H. Sarma.

Discovery of AcrAB-TolC pump inhibitors: Virtual screening and molecular dynamics simulation approach.

AcrAB-TolC tripartite efflux pump, which belongs to the RND superfamily, is a main multi-drug efflux system of Escherichia coli (E. coli) because of the broad resistance on various antibiotics. With the discovering of efflux pump inhibitors (EPIs), a combination between these and antibiotics is one of the most promising therapies. Therefore, building a virtual screening model with prediction capacities for the efflux pump inhibitory activities of candidates from DrugBank and ZINC15 dataset, is one of the key goals of this project. Based on the database of 170 diverse chemical structures collected from 28 research journals, two 2D-QSAR models and a 3D-pharmacophore model have been performed. On the AcrB protein (PDB 4DX7), two binding sites have been discovered that match to the hydrophobic trap in the distal pocket and the switch loop in the proximal pocket. After virtual screening processes, twenty candidate AcrAB-TolC inhibitors have been subjected to molecular dynamics simulations, binding free energy calculations and ADMET predictions. The results indicate that three compounds namely DB09233, DB02581, and DB15224 are potential inhibitors with ΔGbind of -42.30 ± 4.58, -40.76 ± 7.30 and -31.06 ± 7.63 kcal.mol-1, respectively.Communicated by Ramaswamy H. Sarma.

In silico approach to identify novel allosteric intracellular antagonist for blocking the interleukin-8/CXCR2 receptor signaling pathway.

The role of interleukin-8 (IL-8) and its receptor CXCR2 in inflammatory responses and tumor development and progression has been well documented. Our study aims to discover novel compounds as CXCR2 antagonists to block the IL-8 signaling pathway using an in silico drug design. Herein, a structure-based pharmacophore model was developed based on the crystal structure of inactive CXCR2 in a complex with an allosteric inhibitor. This model was validated and refined, followed by virtual screening with the ZINC15 database. Subsequent molecular docking allows for predicting the best pose of a ligand inside a receptor binding site. We found that the 35 top-ranked hits exhibited docking scores from -30.81 to -25.28 kJ/mol and better interaction potential comparing the reference inhibitor. Analysis of ADME and toxicity properties revealed the efficacy and safety of the selected seven compounds. To validate the stability of the protein-ligand complex structure MD simulations approach has also been performed and confirmed via the critical parameters. The MD results explained that the CXCR2 receptor bound with two best-proposed molecules, including ZINC77105530 and ZINC93176465, was quite stable states as observed from low RMSD, RMSF, Rg, SASA values, and high occupancy of the interaction types. Finally, our data identified that these compounds play as potential inhibitors of IL-8 signaling pathways with the MM/GBSA binding free energies of -41.77 ± 6.45 kcal/mol and -38.84 ± 6.16 kcal/mol, respectively.Communicated by Ramaswamy H. Sarma.

Identification of small molecules as potential inhibitors of interleukin 6: a multi-computational investigation.

IL(interleukin)-6 is a multifunctional cytokine crucial for immunological, hematopoiesis, inflammation, and bone metabolism. Strikingly, IL-6 has been shown to significantly contribute to the initiation of cytokine storm-an acute systemic inflammatory syndrome in Covid-19 patients. Recent study has showed that blocking the IL-6 signaling pathway with an anti-IL-6 receptor monoclonal antibody (mAb) can reduce the severity of COVID-19 symptoms and enhance patient survival. However, the mAb has several drawbacks, such as high cost, potential immunogenicity, and invasive administration due to the large-molecule protein product. Instead, these issues could be mitigated using small molecule IL-6 inhibitors, but none are currently available. This study aimed to discover IL-6 inhibitors based on the PPI with a novel camelid Fab fragment, namely 68F2, in a crystal protein complex structure (PDB ID: 4ZS7). The pharmacophore models and molecular docking were used to screen compounds from DrugBank databases. The oral bioavailability of the top 24 ligands from the screening was predicted by the SwissAMDE tool. Subsequently, the selected molecules from docking and MD simulation illustrated a promising binding affinity in the formation of stable complexes at the active binding pocket of IL-6. Binding energies using the MM-PBSA technique were applied to the top 4 hit compounds. The result indicated that DB08402 and DB12903 could form strong interactions and build stable protein-ligand complexes with IL-6. These potential compounds may serve as a basis for further developing small molecule IL-6 inhibitors in the future.

The Effects of One-Point Mutation on the New Delhi Metallo Beta-Lactamase-1 Resistance toward Carbapenem Antibiotics and ß-Lactamase Inhibitors: An In Silico Systematic Approach.

Antibiotic resistance has been becoming more and more critical due to bacteria's evolving hydrolysis enzymes. The NDM-1 enzyme could hydrolyze not only carbapenems but also most of ß-lactam's antibiotics and inhibitors. In fact, variant strains could impose a high impact on the resistance of bacteria producing NDM-1. Although previous studies showed the effect of some variants toward antibiotics and inhibitors binding, there has been no research systematically evaluating the effects of alternative one-point mutations on the hydrolysis capacity of NDM-1. This study aims to identify which mutants could increase or decrease the effectiveness of antibiotics and ß-lactamase inhibitors toward bacteria. Firstly, 35 different variants with a high probability of emergence based on the PAM-1 matrix were constructed and then docked with 5 ligands, namely d-captopril, l-captopril, thiorphan, imipenem, and meropenem. The selected complexes underwent molecular dynamics simulation and free energy binding estimation, with the results showing that the substitutions at residues 122 and 124 most influenced the binding ability of NDM-1 toward inhibitors and antibiotics. The H122R mutant decreases the binding ability between d-captopril and NDM-1 and diminishes the effectiveness of this antibiotic toward Enterobacteriaceae. However, the H122R mutant has a contrary impact on thiorphan, which should be tested in vitro and in vivo in further experiments.

Determination of Antioxidant, Cytotoxicity, and Acetylcholinesterase Inhibitory Activities of Alkaloids Isolated from Sophora flavescens Ait. Grown in Dak Nong, Vietnam.

Traditional/herbal medicine has gained increasing interests recently, especially in Asian countries such as Vietnam, due to its diverse therapeutic actions. In the treasure of Vietnamese medicinal plants, one of the potential herbs is the roots of Sophora flavescens Ait. (SF, "Kho sam" in Vietnamese). However, limited information has been reported on the Vietnamese SF compositions and their respective alkaloids' anti-acetylcholinesterase action. Thus, this study investigated the extractions, isolations, identifications, and in-vitro antioxidant, cytotoxicity, and acetylcholinesterase inhibitory activities, of the SF root extracts and their purified alkaloid compounds. To this end, four pure compounds were successfully isolated, purity-tested by HPLC, and structurally identified by spectroscopic techniques of FTIR, MS, and NMR. These compounds, confirmed to be oxysophocarpine, oxymatrine, matrine, and sophoridine, were then determined their therapeutic actions. The SF extracts and the compounds did not possess significant antioxidant activity using the DPPH and MDA assays, and cytotoxicity action using the MTT assay on the MDA-MB-231 breast cancer cell line. On the other hand, the SF total extract yielded a moderate acetylcholinesterase inhibition effect, with an IC50 of 0.1077 ± 0.0023 mg/mL. In summary, the SF extract demonstrated potential effects as an anti-acetylcholinesterase agent and could be further researched to become a pharmaceutical product for diseases related to acetylcholine deficiency, such as dementia.

Identification of Diosmin and Flavin Adenine Dinucleotide as Repurposing Treatments for Monkeypox Virus: A Computational Study.

The World Health Organization declared monkeypox a global public health emergency on 23 July 2022. This disease was caused by the monkeypox virus (MPXV), which was first identified in 1958 in Denmark. The MPXV is a member of the Poxviridae family, the Chordopoxvirinae subfamily, and the genus Orthopoxvirus, which share high similarities with the vaccinia virus (the virus used to produce the smallpox vaccine). For the initial stage of infection, the MPXV needs to attach to the human cell surface glycosaminoglycan (GAG) adhesion molecules using its E8 protein. However, up until now, neither a structure for the MPXV E8 protein nor a specific cure for the MPXV exists. This study aimed to search for small molecules that inhibit the MPXV E8 protein, using computational approaches. In this study, a high-quality three-dimensional structure of the MPXV E8 protein was retrieved by homology modeling using the AlphaFold deep learning server. Subsequent molecular docking and molecular dynamics simulations (MDs) for a cumulative duration of 2.1 microseconds revealed that ZINC003977803 (Diosmin) and ZINC008215434 (Flavin adenine dinucleotide-FAD) could be potential inhibitors against the E8 protein with the MM/GBSA binding free energies of -38.19 ± 9.69 and -35.59 ± 7.65 kcal·mol-1, respectively.

Exploration of chalcones as 3-chymotrypsin-like protease (3CLpro) inhibitors of SARS-CoV-2 using computational approaches.

The main protease 3CLpro is one of the potential targets against coronavirus. Inhibiting this enzyme leads to the interruption of viral replication. Chalcone and its derivatives were reported to possess the ability to bind to 3CLpro protease in the binding pocket. This study explored an in-house database of 269 chalcones as 3CLpro inhibitors using in silico screening models, including molecular docking, molecular dynamics simulation, binding free energy calculation, and ADME prediction. C264 and C235 stand out as the two most potential structures. The top hit compound C264 was with the Jamda score of -2.8329 and the MM/GBSA binding energy mean value of -28.23 ± 3.53 kcal/mol, which was lower than the reference ligand. Despite the lower mean binding energy (-22.07 ± 3.39 kcal/mol), in-depth analysis of binding interaction suggested C235 could be another potential candidate. Further, in vitro and in vivo experiments are required to confirm the inhibitory ability. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-02000-3.

On Data Augmentation for GAN Training.

Recent successes in Generative Adversarial Networks (GAN) have affirmed the importance of using more data in GAN training. Yet it is expensive to collect data in many domains such as medical applications. Data Augmentation (DA) has been applied in these applications. In this work, we first argue that the classical DA approach could mislead the generator to learn the distribution of the augmented data, which could be different from that of the original data. We then propose a principled framework, termed Data Augmentation Optimized for GAN (DAG), to enable the use of augmented data in GAN training to improve the learning of the original distribution. We provide theoretical analysis to show that using our proposed DAG aligns with the original GAN in minimizing the Jensen-Shannon (JS) divergence between the original distribution and model distribution. Importantly, the proposed DAG effectively leverages the augmented data to improve the learning of discriminator and generator. We conduct experiments to apply DAG to different GAN models: unconditional GAN, conditional GAN, self-supervised GAN and CycleGAN using datasets of natural images and medical images. The results show that DAG achieves consistent and considerable improvements across these models. Furthermore, when DAG is used in some GAN models, the system establishes state-of-the-art Fréchet Inception Distance (FID) scores. Our code is available (https://github.com/tntrung/dag-gans).

Cytotoxic lignans from fruits of Cleistanthus tonkinensis.

Seven new lignans, cleistonkinins A- E (1-5), cleistonkisides A and B (6-7) were isolated from the fruits of Cleistanthus tonkinensis (Euphorbiaceae), together with five known aryltetralin lignans, cleisindoside B (8), cleistantoxin (9), cleisindoside D (10), neocleistantoxin (11) and polygamain (12). Their structures were established from spectral analysis, including mass spectrometry and 2D-NMR. The absolute configurations of 4-7 were determined by analysis of their experimental CD spectra and comparison with calculated electronic circular dichroism (ECD) spectra. Compounds 2 and 6 had selective inhibition with moderate cytotoxicity against Pan C1 and A549 cell lines, respectively. Cleistantoxin (9) was significantly active against A549, HeLa, Hep3B, Pan C1 and MCF7 cell lines while it was less cytotoxic against HeLa cells. Neocleistantoxin (11) exhibited remarkable inhibition toward A549, HeLa, MCF7 and Pan C1. This is the first report for cytotoxicity of 9 and 11 against A549, Hep3B and Pan C1 cell lines.

Lanostane Triterpenoids from Ganoderma tropicum Collected in Vietnam and Their Nitroblue Tetrazolium Reductive Activity In Vitro

A new compound, 3β-acetoxylanosta-7,9(11),24-triene-26-al (3), and seven known compounds (1 – 2 and 4 – 8) were isolated from Ganoderma tropicum (Jung.) Bres. collected in Tay Nguyen, Vietnam. The structures of these compounds were determined by one- and two-dimensional nuclear magnetic resonance spectroscopy, electrospray ionization mass spectrometry (ESI-MS), and high-resolution ESI-MS, and by comparison with literature data. All of the isolated compounds were tested for nitroblue tetrazolium (NBT) reduction activity in Saccharomyces cerevisiae-stimulated RAW 246.7 cells. Among them, compounds 2 – 4 and 6 – 8 enhanced the NBT reduction in a dose-dependent manner.

Lanostane Triterpenoids from Ganoderma tropicum Collected in Vietnam and Their Nitroblue Tetrazolium Reductive Activity In Vitro

A new compound, 3β-acetoxylanosta-7,9(11),24-triene-26-al (3), and seven known compounds (1 – 2 and 4 – 8) were isolated from Ganoderma tropicum (Jung.) Bres. collected in Tay Nguyen, Vietnam. The structures of these compounds were determined by one- and two-dimensional nuclear magnetic resonance spectroscopy, electrospray ionization mass spectrometry (ESI-MS), and high-resolution ESI-MS, and by comparison with literature data. All of the isolated compounds were tested for nitroblue tetrazolium (NBT) reduction activity in Saccharomyces cerevisiae-stimulated RAW 246.7 cells. Among them, compounds 2 – 4 and 6 – 8 enhanced the NBT reduction in a dose-dependent manner.

An uncommon therapeutic option for a challenging cause of pleural effusion.

Can you diagnose this challenging cause of pleural effusion? http://bit.ly/2VVwZv3.

Predicting antigenic variants of H1N1 influenza virus based on epidemics and pandemics using a stacking model.

H1N1 is the earliest emerging subtype of influenza A viruses with available genomic sequences, has caused several pandemics and seasonal epidemics, resulting in millions of deaths and enormous economic losses. Timely determination of new antigenic variants is crucial for the vaccine selection and flu prevention. In this study, we chronologically divided the H1N1 strains into several periods in terms of the epidemics and pandemics. Computational models have been constructed to predict antigenic variants based on epidemic and pandemic periods. By sequence analysis, we demonstrated the diverse mutation patterns of HA1 protein on different periods and that an individual model built upon each period can not represent the variations of H1N1 virus. A stacking model was established for the prediction of antigenic variants, combining all the variation patterns across periods, which would help assess a new influenza strain's antigenicity. Three different feature extraction methods, i.e. residue-based, regional band-based and epitope region-based, were applied on the stacking model to verify its feasibility and robustness. The results showed the capability of determining antigenic variants prediction with accuracy as high as 0.908 which performed better than any of the single models. The prediction performance using the stacking model indicates clear distinctions of mutation patterns and antigenicity between epidemic and pandemic strains. It would also facilitate rapid determination of antigenic variants and influenza surveillance.

LIDAR Assist Spatial Sensing for the Visually Impaired and Performance Analysis.

Echolocation enables people with impaired or no vision to comprehend the surrounding spatial information through the reflected sound. However, this technique often requires substantial training, and the accuracy of echolocation is subject to various conditions. Furthermore, the individuals who practice this sensing method must simultaneously generate the sound and process the received audio information. This paper proposes and evaluates a proof-of-concept light detection and ranging (LIDAR) assist spatial sensing (LASS) system, which intends to overcome these restrictions by obtaining the spatial information of the user's surroundings through a LIDAR sensor and translating the spatial information into the stereo sound of various pitches. The stereo sound of relative pitch represents the information regarding objects' angular orientation and horizontal distance, respectively, thus granting visually impaired users an enhanced spatial perception of his or her surrounding areas and potential obstacles. This paper is divided into two phases: Phase I is to engineer the hardware and software of the LASS system and Phase II focuses on the system efficacy study. The study, approved by the Penn State Institutional Review Board, included 18 student volunteers, who were recruited through the Penn State Department of Psychology Subject Pool. This paper demonstrates that the blindfolded individuals equipped with the LASS system are able to quantitatively identify the surrounding obstacles, differentiate their relative distance, and distinguish the angular location of multiple objects with minimal training.

Investigation on residual quantities of some insecticides on some medicinal plants cultivated at Nghia Trai hamlet, Tan Quang commune, Hung Yen province

In 6 simples of Nga Truat. 2 simples of Dia Lien, 2 samples of Cu Coc collected in Nghia Trai village. There was no-orgam chlorine pollutants; but in 1 of 9 samples of camomille containing cypermethrine residue exceeded the normal standard

Elaboration of analytic method and preliminary results of initial investigation on chemical residues of chloro-organo-pesticides in Sanchi (Panax pseudoginseng Wall)

A solid phase extraction (SPE) and GC-ECD for multi-residues determination of 14 organo-chlorinated pesticides (OCPs) in radix Pseudo-ginseng were introduced. Using n-hexane as extracting solvent and silica gel for clean up of sample extract, with GC-ECD analysis, good separation of 14 OCPs and carbophenothion(IS) was achieved on capillary column coated with poly(5% diphenyl) siloxane. Experiments showed that n-hexane is adequate as extracting solvent(percentage of recovery70% for 13 in total 14 analyses), the LOD was about 0.35 to 1.6 ppb for blank sample spiked with standards. The method has been carried out on 7 samples collected from market for preliminary investigation of its actual OCPs residues. For 14 OCPs being analysed, results showed that all samples to be examined are complied with requirements of MRL in USP 24 or in Eur. P97.We may conclude that those samples were cultivated in less contaminated soils or none of 14 OCPs was still in illegal use