cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Insight parameter drug design for human β-tryptase inhibition integrated molecular docking, QSAR, molecular dynamics simulation, and pharmacophore modelling studies of α-keto-[1,2,4]-oxadiazoles
Creators: name: Yu, Chai Xin
name: Tan, Jian Wei
name: Rullah, Kamal
name: Imran, Syahrul
name: Tham, Chau Ling
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: Dengue hemorrhagic fever (DHF) is severe dengue with a hallmark of vascular leakage. β-tryptase has been found to promote vascular leakage in DHF patients, which could be a potential target for DHF treatment. This study aims to develop a theoretical background for designing and selecting human β-tryptase inhibitors through computational studies. Thirty-four α-keto-[1,2,3]-oxadiazoles scaffold-based compounds were used to generate 2D-QSAR models and for molecular docking studies with β-tryptase (PDB Code 4A6L). In addition, molecular dynamics (MD) simulation and molecular mechanics generalised born surface area (MM-GBSA) analysis on the binding of the reported most active compound, compound 11e, towards β-tryptase were performed. Finally, a structure-based pharmacophore model was generated. The selected 2D-QSAR models have statistically proven good models by internal and external validation as well as the y-randomization test. The docking results of compound 11e showed lower CDOCKER energy than the 4A6L co-crystallised ligand and a similar binding pattern as the 4A6L co-crystallised ligand. From molecular dynamics simulation, 4A6L in compound 11e bound state has RMSD below 2 Å throughout the 500 ns simulation, indicating the docked complex is stable. Besides, MM-GBSA analysis suggested the 4A6L-compound 11e docked complex (−66.04 Kcal/mol) is structurally as stable as the 4A6L-native ligand co-crystallized structure (−66.84 Kcal/mol). The best pharmacophore model identified features included hydrogen bond acceptor, ionic interaction, hydrophobic interaction, and aromatic ring, which contribute to the inhibitory potency of a compound. This study supplied insight and knowledge for developing novel chemical compounds with improved inhibition of β-tryptase. Communicated by Ramaswamy H. Sarma
Understanding Pregnancy and Childbirth Experiences Among Adolescents in Baguio City
Creators: name: Malingta, Teresita Opate
Publisher: name: Zenodo
Year: 2010
Subjects: Adolescent pregnancy
Childbirth experience
Phenomenology

description: Objective: To understand the lived experience of adolescent mothers with regard to their pregnancy and childbirth. Study design and methods: Phenomenological study of 7 adolescent mothers. Results: Themes that emerged from the conversation with the mothers were (a) finding encouragement, (b) the downside of my childbirth experience, (c) point of no return, and (d) hope for the time to come. The participants found encouragement from their child from their immediate family, from the father of their baby for the married and those who are in committed relationship, from life’s changes and from themselves. The negative aspect of their childbirth experience includes having to stop their studies, strained relationship with their own fathers and the father of the child for the three single adolescent mothers. Difficulties arise from burden of childcare, childcare during illness, breastfeeding and financial dependency. Loss of my youth where the participants were into maturity as they perform adult roles and feeling sort were the other categories under the theme downside of my experience. A recollection of the past is described in the theme point of no return. Family problems, bad influence and wrong choices were the precursors to unintended pregnancy. Fears of the consequences of pregnancy and thoughts of abortion demonstrated that the pregnancies were unintended. Emotions felt during labor and delivery were pain, fear, loss of patience and relief. The health workers comments, instructions and actions made an impact on the labor and delivery experiences of the adolescent mothers. The theme hopes for the time that is to achieve all that they hope for their child and their own selves. Clinical implications: Medical and nursing interventions should address all section in the framework. Interventions to prevent adolescent pregnancy should be of utmost importance. However, when pregnancy occurs the adolescent should be helped from pregnancy onwards. Need of support person, efforts to lessen the pain and attempts to address the fears of the adolescent during labor and delivery can greatly improve her childbirth experience. Adolescent mothers can benefit from the services rendered by health workers when they display a more caring attitude that includes providing nonjudgmental care despite the adolescent’s lifestyle choices, being available and maintaining a presence for constant support and allowing the adolescent to be part of the decision-making process when possible.

description: Masters Thesis
Monitoring the Impact of Social Policy, 1980–2001: Social Expenditure Patterns in Aotearoa / New Zealan
Creators: name: Cotterell, Gerard
name: Crothers, Charles
Publisher: name: The University of Auckland
Year: 2015
Subjects: subject: Sociology
subject: FOS: Sociology

description: The paper examines social spending in New Zealand over the period 1981 - 2001 using OECD social expensditure data
Structural elucidation of ETHR-A and ETHR-B from Plutella xylostella and insight into non-conservative mutations in transmembrane helix-6
Creators: name: Patidar, Ishwar
name: Palaka, Bhagath Kumar
name: Katike, Umamahesh
name: Ilavarasi, Anbumani Velmurugan
name: Tulsi
name: Mohanty, Saswati Sarita
name: Ampasala, Dinakara Rao
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Evolutionary Biology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: The development of Diamondback moth (DBM) depends on the ecdysis triggering hormone receptor (ETHR); a neuronal membrane G-protein coupled receptor (GPCR) connected to the metamorphosis cascade. Lepidopteran insect DBM is an infamous pest of cruciferous plants. This study examined the full-length coding sequences (CDS) of PxETHR-A and PxETHR-B from the DBM genome. The three-dimensional (3 D) models of both receptors were generated in an inactive state. The behaviour and stability of receptors were examined using molecular dynamics simulations in a lipid membrane system for 300 ns and established a GPCR family-based view. Secondary interactions within receptors were studied to know more about factors contributing to their stability. Multiple sequence alignment revealed conserved features of insect ETHRs those compared to the GPCR family proteins. These features were helpful during the evaluation of the molecular models of both receptors. Side-chain orientation of conserved residues, non-conserved and conserved hydrogen-bond networks (HBN) and hydrophobic clusters were examined in the structures of both receptors. The non-conserved residues L6.35, T6.39, C/S6.43, and L6.48, are present in a conserved position on the transmembrane helix-6 (TM6) of ETHRs. In TM6, PxETHR-A and PxETHR-B differ at positions C/S6.43 and Y/F6.51, both being part of the HBN. Communicated by Ramaswamy H. Sarma
Pseudo Panel Data Models with Cohort Interactive Effects
Creators: name: Artūras Juodis
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Science Policy
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Mathematics
subject: FOS: Mathematics
subject: Biological Sciences
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Biotechnology

description: When genuine panel data samples are not available, repeated cross-sectional surveys can be used to form so-called pseudo panels. In this paper, we investigate the properties of linear pseudo panel data estimators with fixed number of cohorts and time observations. We expand the setup of Inoue (2008) to models with factor residuals by adapting the approach of Ahn et al. (2013) for genuine panels. In a Monte Carlo study we find that the proposed procedure has good finite sample properties in situations with endogeneity, cohort interactive effects and near non-identification. Finally, as an illustration the proposed method is applied to data from Ecuador to study labour supply elasticity.
The natural product content of the selected Cabernet Franc wine samples originating from Serbia: a case study of phenolics
Creators: name: Pejin, Boris
name: Stanimirovic, Bojana
name: Vujovic, Dragan
name: Djordjevic, Jelena Popovic
name: Velickovic, Milovan
name: Vele Tesevic
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Hematology
subject: Plant Biology

description: This work aimed to evaluate the content of selected phenolic natural products in the wine samples made of three new Serbian Cabernet Franc clones (Nos. 02, 010 and 012, respectively) and mother vine (used as the relevant standard) during the period 2008–2012. Compared with all other wine samples, the Cabernet Franc wine of the clone No. 010 was found to have the highest total content of polyphenolics (1.85 ± 0.02 g/L) and anthocyanins (178.55 ± 3.75 mg/L). In addition, its Folin–Ciocalteu index (36.86 ± 0.12) stood out among the examined samples. Finally, the same wine was enriched with ellagic and gallic acids (3.44 ± 0.29 and 27.46 ± 0.21 mg/L, respectively), catechin (135.16 ± 6.47 mg/L) and epicatechin (51.33 ± 2.33 mg/L), the natural products known to exert significant lipid-lowering effects. Taken all together, the clone No. 010 developed in Serbia may offer new Cabernet Franc wine with geographical indication.
Chinese version of "Ten quick tips for machine learning in computational biology"
Creators: name: Chicco, Davide
Publisher: name: Zenodo
Year: 2020
Subjects: machine learning
bioinformatics
computational biology
Chinese translation

description: Translation into Simplified Chinese of the paper "Ten quick tips for machine learning in computational biology", done by volunteers of the EpiMan.cn forum coordinated by Qiguo Lian (Shanghai Institute of Planned Parenthood Research) and reviewed by Yun Niu (Krembil Research Institute). Original version in English: https://doi.org/10.1186/s13040-017-0155-3
Molecular modelling, synthesis and biological evaluation of peptide inhibitors as anti-angiogenic agent targeting neuropilin-1 for anticancer application
Creators: name: Ezatul E. Kamarulzaman
name: Vanderesse, Régis
name: Gazzali, Amirah M.
name: Barberi-Heyob, Muriel
name: Boura, Cédric
name: Frochot, Céline
name: Shawkataly, Omar
name: Aubry, André
name: Habibah A. Wahab
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Vascular endothelial growth factor (VEGF) and its co-receptor neuropilin-1 (NRP-1) are important targets of many pro-angiogenic factors. In this study, nine peptides were synthesized and evaluated for their molecular interaction with NRP-1 and compared to our previous peptide ATWLPPR. Docking study showed that the investigated peptides shared the same binding region as shown by tuftsin known to bind selectively to NRP-1. Four pentapeptides (DKPPR, DKPRR, TKPPR and TKPRR) and a hexapeptide CDKPRR demonstrated good inhibitory activity against NRP-1. In contrast, peptides having arginine residue at sites other than the C-terminus exhibited low activity towards NRP-1 and this is confirmed by their inability to displace the VEGF165 binding to NRP-1. Docking study also revealed that replacement of carboxyl to amide group at the C-terminal arginine of the peptide did not affect significantly the binding interaction to NRP-1. However, the molecular affinity study showed that these peptides have marked reduction in the activity against NRP-1. Pentapeptides having C-terminal arginine showed strong interaction and good inhibitory activity with NRP thus may be a good template for anti-angiogenic targeting agent.
Exploring staphylococcal superantigens to design a potential multi-epitope vaccine against Staphylococcus aureus: an in-silico reverse vaccinology approach
Creators: name: Rahman, Shakilur
name: Sarkar, Kasturi
name: Das, Amit Kumar
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Staphylococcus aureus is a horrifying bacteria capable of causing millions of deaths yearly across the globe. A major contribution to the success of S. aureus as an ESKAPE pathogen is the abundance of virulence factors that can manipulate the innate and adaptive immune system of the individual. Currently, no vaccine is available to treat S. aureus-mediated infections. In this study, we present in-silico approaches to design a stable, safe and immunogenic vaccine that could help to control the infections associated with the bacteria. Three vital pathogenic secreted toxins of S. aureus, such as staphylococcal enterotoxin A (SEA), staphylococcal enterotoxin B (SEB), Toxic-shock syndrome toxin (TSST-1), were selected using the reverse vaccinology approach to design the multi-epitope vaccine (MEV). Linear B-lymphocyte, cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes were predicted from these selected proteins. For designing the multi-epitope vaccine (MEV), B-cell epitopes were joined with the KK linker, CTL epitopes were joined with the AAY linker, and HTL epitopes were joined with the GPGPG linker. Finally, to increase the immune response to the vaccine, a human β-defensin-3 (hBD-3) adjuvant was added to the N-terminus of the MEV construct. The final MEV was found to be antigenic and non-allergen in nature. In-silico immune simulation and cloning analysis predicted the immune-stimulating potential of the designed MEV construct along with the cloning feasibility in the pET28a(+) vector with the E. coli expression system. This immunoinformatics study provides a platform for designing a suitable, safe and effective vaccine against S. aureus. Communicated by Ramaswamy H. Sarma
Methotrexate-conjugated quantum dots: synthesis, characterisation and cytotoxicity in drug resistant cancer cells
Creators: name: Johari-Ahar, Mohammad
name: Barar, Jaleh
name: Alizadeh, Ali Mohammad
name: Soodabeh Davaran
name: Omidi, Yadollah
name: Mohammad-Reza Rashidi
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Hematology

description: Methotrexate (MTX), a folic acid derivative, is a potent anticancer used for treatment of different malignancies, but possible initiation of drug resistance to MTX by cancer cells has limited its applications. Nanoconjugates (NCs) of MTX to quantum dots (QDs) may favour the cellular uptake via folate receptors (FRs)-mediated endocytosis that circumvents the efflux functions of cancer cells. We synthesised MTX-conjugated l-cysteine capped CdSe QDs (MTX-QD nanoconjugates) and evaluated their internalisation and cytotoxicity in the KB cells with/without resistancy to MTX. The NCs were fully characterised by high resolution transmission electron microscopy (HR-TEM), atomic force microscopy (AFM), dynamic light scattering (DLS) and optical spectroscopy. Upon conjugation with MTX, the photoluminescence (PL) properties of QDs altered, while an obvious quenching in PL of QDs was observed after physical mixing. The MTX-QD nanoconjugates efficiently internalised into the cancer cells, and induced markedly high cytotoxicity (IC50, 12.0 µg/mL) in the MTX-resistant KB cells as compared to the free MTX molecules (IC50,105.0 µg/mL), whereas, these values were respectively about 7.0 and 0.6 µg/mL in the MTX-sensitive KB cells. Based on these findings, the MTX-QD nanoconjugates are proposed for the targeted therapy of MTX-resistant cancers, which may provide an improved outcome in the relapsed FR-overexpressing cancers.
A high or a reasonably-reactively elevated platelet-to-lymphocyte ratio, which plays the role?
Creators: name: Xianchun Meng
name: Wanhai Wang
name: Gaohui Wei
name: Chang, Qian
name: Fucheng He
name: Ming, Liang
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: A high or a reasonably-reactively elevated platelet-to-lymphocyte ratio, which plays the role?
Valproic acid induces NET cell growth arrest and enhances tumor suppression of the receptor-targeted peptide–drug conjugate via activating somatostatin receptor type II
Creators: name: Lichun Sun
name: Qingqing Qian
name: Guangchun Sun
name: L. Vienna Mackey
name: Fuselier, Joseph A.
name: Coy, David H.
name: Cui-Yun Yu
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer

description: Background: Human pancreatic carcinoids, a type of neuroendocrine tumors, are asymptomatic and difficult to diagnose, with the effects of traditional anti-cancer therapies being limited. The histone deacetylase (HDAC) inhibitor valproic acid (VPA) was evaluated for its effects alone and in combination with receptor-targeting peptide–drug conjugate via increasing drug internalization. Materials and methods: The in vitro and in vivo assays were used to evaluate the effects of VPA and somatostatin receptor-targeting camptothecin–somatostatin conjugate (CPT-SST). Results: VPA induced proliferation suppression, cell apoptosis and cell cycle arrest. VPA acts as a HDAC inhibitor to induce a decrease of HDAC4 and an increase of acetylated histone 4 (AcH4). Meanwhile, most importantly, besides activating Notch signaling, VPA was observed to stimulate the expression of somatostatin receptor type 2 (SSTR2) that has been applied for receptor-targeting therapies. This characteristic was used for a combination therapy of VPA and CPT-SST. The combination displayed much more potent anti-tumor effects on carcinoid tumor growth by increasing SSTR2 density and drug internalization in target tumor cells. Conclusion: The combination of VPA and a SSTR2-targeting agent provides us a promising approach in treatment of carcinoid tumors.
Allosteric modulation of conserved motifs and helices in 5HT2BR: Advances drug discovery and therapeutic approach towards drug resistant epilepsy
Creators: name: Chauhan, Arushi
name: Sangwan, Namrata
name: Singh, Jitender
name: Prakash, Ajay
name: Medhi, Bikash
name: Avti, Pramod K.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Molecular Biology
Neuroscience
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Hematology
Computational Biology

description: The 5HT2BR, class-A GPCR is a new target, and its significance for seizure reduction in Dravet syndrome is just now gaining interest, suggesting its specific role in epileptic seizure management. Homology modeling of human 5HT2BR (P41595), was performed using a template 4IB4, the modeled structure was cross-validated (stereo chemical hindrance, Ramachandran plot, enrichment analysis) to mimic a closer native structure. Virtual screening (8532 compounds), drug-likeliness, mutagenicity, and carcinogenicity profiling prioritized six compounds for molecular dynamics (500 ns), Rgyr, DCCM. The receptor’s C-alpha fluctuation upon bound agonist (6.91 Å), known antagonist (7.03 Å), and LAS 52115629 (5.83 Å) binding varies, leading to receptor stabilization. The residues C-alpha side-chain in active site strongly interacts (hydrogen bonds) with bound agonist (100% interaction: ASP135), known antagonist (95%:ASP135), and LAS 52115629 (100%:ASP135). The Rgyr for receptor-ligand complex, LAS 52115629 (25.68 Å), lies close to bound agonist-Ergotamine, and DCCM analysis also shows strong positive correlations for LAS 52115629 as compared to known drugs. LAS 52115629 is less likely to cause toxicity than known drugs. The structural parameters in the modeled receptor’s conserved motifs (DRY, PIF, NPY) were altered for receptor activation upon ligand-binding, which otherwise was in the in-activated state. The ligand (LAS 52115629)-binding further alters the helices-III, V, VI (G-protein bound), and VII, which form potential interacting sites with the receptor and are proven necessary for activating the receptor. Therefore, LAS 52115629 can act as a potential 5HT2BR agonist, targeting drug-resistant epilepsy. Communicated by Ramaswamy H. Sarma
Synthesis, molecular docking and dynamics studies of pyridazino[4,5-b]quinoxalin-1(2H)-ones as targeting main protease of COVID-19
Creators: name: Moghimi, Parvin
name: Sabet-Sarvestani, Hossein
name: Shiri, Ali
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified

description: The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a crisis in public health. Because, the 3CLpro, the main protease of SARS-CoV-2, possesses a critical role in coronavirus replication, many efforts have been devoted to developing various inhibitors to prevent the fast spread of COVID-19. In the current work, a number of various pyridazino[4,5-b]quinoxalin-1(2H)-one derivatives bearing thiadiazine and thiadiazole fragments has been prepared via a straightforward and practical strategy involving the reaction of 2-(ethoxycarbonyl)-3-formylquinoxaline 1,4-dioxide with thiocarbohydrazide under reflux conditions. To determine the bioavailability of pyridazino[4,5-b]quinoxalin-1(2H)-one derivatives, Lipinski’s rule of five has been carried out. Regarding this rule, none of the synthesized compounds exhibit any deviation from Lipinski’s rule of five. Furthermore, molecular docking and molecular dynamics approaches have been implemented to figure out the potential interactions of products with SARS-CoV-2 main protease. The outcomes of molecular docking studies demonstrate that the phenyl and nitrophenyl substituted pyridazino[4,5-b]quinoxalin-1(2H)-one show the lowest binding affinity among the other compounds, indicating a favorable orientation in the active site of the chymotrypsin-like cysteine protease. In addition, the MD simulation performed to evaluate the stability of the protein–ligand complex represents that the average binding energy of the nitrophenyl complex is less than that of the phenyl complex. Therefore, according to the in silico results, the inhibitory effect of the nitrophenyl complex is more significant than the phenyl complex. Communicated by Ramaswamy H. Sarma
New molecular insights for 4H-1,2,4-triazole derivatives as inhibitors of tankyrase and Wnt-signaling antagonist: a molecular dynamics simulation study
Creators: name: Mehta, Chirag C.
name: Rohit, Shishir
name: Patel, Saumya
name: Bhatt, Hardik G.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified

description: Tankyrase (TNKS) enzymes remained central biotargets to treat Wnt-driven colorectal cancers. The success of Olaparib posited the druggability of PARP family enzymes depending on their role in tumor proliferation. In this work, an MD-simulation-based comparative assessment of the protein–ligand interactions using the best-docked poses of three selected compounds (two of the designed and previously synthesized molecules obtained through molecular docking and one reported TNKS inhibitor) was performed for a 500 ns period. The PDB:ID-7KKP and 3U9H were selected for TNKS1 and TNKS2, respectively. The Molecular Mechanics Generalized Born Surface Area (MM-GBSA) based binding energy data exhibited stronger binding of compound-15 (average values of −102.92 and −104.32 kcal/mol for TNKS1 and TNKS2, respectively) as compared to compound-22 (average values of −82.99 and −85.68 kcal/mol for TNKS1 and TNKS2, respectively) and the reported compound-32 (average values of −81.89 and −74.43 kcal/mol for TNKS1 and TNKS2, respectively). Compound-15 and compound-22 exhibited comparable or superior binding to both receptors forming stable complexes when compared to that of compound-32 upon examining their MD trajectories. The key contributors were hydrophobic stacking and optimum hydrogen bonding allowing these molecules to occupy the adenosine pocket by interfacing D-loop residues. The results of bond distance analysis, radius of gyration, root mean square deviation, root mean square fluctuation, snapshots at different time intervals, LUMO–HUMO energy differences, electrostatic potential calculations, and binding free energy suggested better binding efficiency for compound-15 to TNKS enzymes. The computed physicochemical and ADMET properties of compound-15 were encouraging and could be explored further for drug development. Communicated by Ramaswamy H. Sarma
Microemulsions mediated effective delivery of methotrexate hydrogel: more than a tour de force in psoriasis therapeutics
Creators: name: Basant Amarji
name: Garg, Neeraj K.
name: Singh, Bhupinder
name: Katare, Om Prakash
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Methotrexate (MTX), a well known drug for the treatment of cancer and rheumatoid arthritis, has gained prominence in the treatment of psoriasis over the period of years. However, the present mode of systemic administration through oral or parenteral route has always proposition, full of compromises. The toxicity of drug to the vital organs and physiological environment is the major concern. Also, its poor skin penetration is one major problem. Hence novel system based on lipid carriers has been considered here to overcome the barriers. Microemulsions (MEs) were prepared using pseudo-ternary phase diagram (PTPD) and they were characterized for various parameters such as size, shape (cryo-SEM), PDI, zeta potential, etc. The chosen MEs system (optimized) was then incorporated into secondary vehicles and characterized for rheological behavior, texture profile analysis, in vitro release, ex vivo permeation and drug distribution into different layers of skin. The developed formulations were further evaluated in ex vivo and in vivo such as cell line study, imiquimod-induced psoriatic model, allergic contact dermatitis, rat tail model (% orthokeratosis) and safety test (Draize test). The MEs based MTX gel has shown its potential in locating the drug at the desired domain of stratum corneum, epidermal and dermal layers of skin and reducing systemic absorption. Our results are suggestive of MEs potential as a novel carrier for topical delivery of MTX in topical therapeutic and safety approaches. In conclusion, developed MEs-based hydrogel has shown promising results in achieving effective delivery of MTX.
Molecular modelling, synthesis and biological evaluation of peptide inhibitors as anti-angiogenic agent targeting Neuropilin-1 for anticancer application
Creators: name: Vanderesse, Régis
name: Barberi-Heyob, Muriel
name: Frochot, Céline
name: Ezatul E. Kamarulzaman
name: Gazzali, Amirah M.
name: Boura, Cédric
name: Shawkataly, Omar
name: Aubry, André
name: Habibah A Wahab
Publisher: name: Taylor & Francis
Year: 2016
Subjects: Biological Sciences
Chemistry
Biotechnology
Pharmacology
Molecular Biology
Biochemistry
Biophysics

description: VEGF and its co-receptor neuropilin-1 (NRP-1) are important targets of many pro-angiogenic factors. In this study, nine peptides were synthesized and evaluated for their molecular interaction with NRP-1 and compared to our previous peptide ATWLPPR. Docking study showed that the investigated peptides shared the same binding region as shown by tuftsin known to bind selectively to neuropilin-1. Four pentapeptides (DKPPR, DKPRR, TKPPR and TKPRR) and a hexapeptide CDKPRR demonstrated good inhibitory activity against NRP-1. In contrast, peptides having arginine residue at sites other than the C-terminus exhibited low activity towards NRP-1 and this is confirmed by their inability to displace the VEGF165 binding to NRP-1. Docking study also revealed that replacement of carboxyl to amide group at the C-terminal arginine of the peptide did not affect significantly the binding interaction to NRP-1. However, the molecular affinity study showed that these peptides have marked reduction in the activity against NRP-1. Pentapeptides having C-terminal arginine showed strong interaction and good inhibitory activity with NRP thus may be a good template for anti-angiogenic targeting agent.
Structure-based virtual screening of novel natural products as chalcone derivatives against SARS-CoV-2 Mpro
Creators: name: Aissouq, Abdellah El
name: Bouachrine, Mohammed
name: Bouayyadi, Lahcen
name: Ouammou, Abdelkrim
name: Khalil, Fouad
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from spreading, but there are currently no approved medicines to treat COVID-19. In this work, a dataset of 142 natural products collected from various medicinal plants was used to perform structure-based virtual screening (SBVS) through the combined application of molecular docking and molecular dynamics (MD) simulation methods. First, the dataset of compounds was optimized using the density functional theory (DFT) approach. The optimized compounds were then submitted to the first screening, which was done by the pKCM web server to look for drug-likeness and the PyRx to look for binding affinity. Among the 142 natural substances, 10 compounds were selected for docking validation. Compounds that interact with CYS145 and LEU141, the essential catalytic residues, as well as compounds with binding affinities less than −8.0 kcal/mol, are considered promising anti-SARS-CoV-2 drug candidates. The top-ranked compounds were then evaluated by MD simulations and MM-GBSA method. These results could help researchers come up with new natural compounds that could be used to treat SARS-CoV-2. Communicated by Ramaswamy H. Sarma
Self-assembly of thiacyanine dyes in water for the synthesis of active hybrid nanofibres
Creators: name: Govindaswamy Shanker
name: Gurumurthy Hegde
name: Rodriguez-Abreu, Carlos
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Inorganic Chemistry

description: Water-soluble self-assembled nanostructures were synthesised by simple counter ion exchange of thiacyanine dyes which helps in the formation of nematic (N) and hexagonal (M) chromonic liquid-crystalline (CLCs) phases. Conjugated double bonds as central spacers connected between two benzothiazole segments affect water solubility and liquid crystal formation. Aggregation-dependent properties characterised by ultraviolet–visible, fluorescence and 1H nuclear magnetic resonance spectroscopy. Sol–gel reaction of dye aggregates with silica species furnishes entangled nanotubular fibres with constant diameter and their length in excess of micrometres, having templates of pore sizes below the mesoporous range. The π–π stacked chromonic aggregate dyes are also of importance in shape selective catalysis, adsorption, desorption micro-patterned materials, and provide a significant step towards biosensor medical applications because of their water-soluble nature.
DFT calculations, molecular docking, in vitro antimicrobial and antidiabetic studies of green synthesized Schiff bases: as Covid-19 inhibitor
Creators: name: G., Saranya
name: K., Devendraprasad
name: P., Shanmugapriya
name: N., Bhuvaneshwari
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: In this investigation, we synthesized Schiff bases 2-(2-methoxyphenoxy)-N-(4-methylbenzylidene)ethanamine, N-(4-methoxybenzylidene)-2-(2-methoxyphenoxy)ethanamine and 2-(2-methoxyphenoxy)-N-(4-nitrobenzylidene)ethanamine from 2-(2-methoxyphenoxy)ethanamine and various aromatic aldehydes by the environmentally friendly sonication method. The B3LYP method with a 6-311++G (d, p) basis set was used in the DFT calculation to obtain the optimized structure of the Schiff base MPEA-NIT. The compounds were tested in vitro for inhibition of bacterial growth (disc well method) and inhibition of α-amylase (starch-iodine method). The compounds tested showed inhibitory activities. In addition, they were subjected to PASS analysis, drug likeness, and bioactivity score predictions using online software. To confirm the experimental findings, molecular docking analyses of synthesized compounds on α-amylase (PDB ID: 1SMD), tRNA threonylcarbamoyladenosine (PDB ID: 5MVR), glycosyl transferase (PDB ID: 6D9T), and peptididoglycan D,D-transpeptidase (PDB ID: 6HZQ) were performed. The emergence of a new coronavirus epidemic necessitates the development of antiviral medications (SARS-CoV-2). Docking active site interactions were investigated to predict compounds’ activity against COVID-19 by binding with the SARS-CoV-2 (PDB ID: 6Y84). Communicated by Ramaswamy H. Sarma
Synthesis, in silico, in vitro and in vivo studies of novel natural-based arylidenes curcumin as potential glycohydrolase digestive enzymes inhibitors
Creators: name: Ezati, Mohammad
name: Ghavamipour, Fahimeh
name: Yazdi, Mohammad Mahdi Hassan
name: Sadrjavadi, Komail
name: Sajedi, Reza H.
name: Adibi, Hadi
name: Khodarahmi, Reza
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Diabetes is one of the most common metabolic diseases in humans and the use of herbal medicines is of great clinical importance to inhibit carbohydrate-hydrolyzing enzymes and reduce blood glucose levels in diabetic patients. Inhibition of glycosidase activity is an effective way to treat and prevent diabetes. Therefore, in this study, curcumin-based benzaldehyde derivatives were synthesized and used as influential agents in the treatment of diabetes with inhibitory properties against two carbohydrate-hydrolyzing enzymes α-glucosidase (α-Glu) and α-amylase (α-Amy) as significant therapeutic targets for reducing postprandial hyperglycemia. Overall, the findings showed that due to the specific inhibitory activity against α-Glu in comparison with α-Amy, as well as more stability and antioxidant activity than curcumin, C5 and C8 derivatives are potentially important anti-diabetic drugs, not only to decrease glycemic index but also to limit the activity of the main production pathways of reactive oxygen species (ROS) in diabetic patients. Communicated by Ramaswamy H. Sarma
A single parameter determines mesophase transitions in Swollen Liquid Crystals
Creators: name: Kinadjian, Natacha
name: Nallet, Frédéric
name: Ly, Isabelle
name: Bentaleb, Ahmed
name: Rénal Backov
name: Prouzet, Eric
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: We report how the control of a single parameter, the co-surfactant, determines the phase transitions of oil-in-water swollen liquid crystals (SLCs) prepared with cetyltrimethylammonium bromide (CTAB), from cubic to hexagonal, lamellar, and finally sponge-like structures. SLCs are complex mixtures (surfactant + co-surfactant + water + salt + oil) usually prepared to form hexagonal mesophases, with cell parameters tunable between 3 and 30 nm. These hexagonal mesophases were successfully used as nanoreactors to prepare a broad range of nanostructured materials. Because the potential of these mesophases as adaptive nanoreactors has not been extended to other liquid crystal geometries than the hexagonal, we studied in a first step the structure evolution of SLCs made with CTAB, cyclohexane, pentanol-1, water and different stabilising salts. We used small-angle X-ray scattering (SAXS), polarised light microscopy and Freeze-Fracture TEM to provide a partial phase diagram and list the different mesophases obtained as a function of composition. We report that the adjustment of a single parameter, the co-surfactant (pentanol-1), determines the phase transition between cubic, hexagonal, lamellar, and sponge-like structures, all other parameters such as the nature and concentration of salt, or amount of oil being constant.
Screening of dietary antioxidants against mitochondria-mediated oxidative stress by visualization of intracellular redox state
Creators: name: Maharjan, Sunita
name: Sakai, Yasuyoshi
name: Hoseki, Jun
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Computational Biology

description: Mitochondrial impairment and the resulting generation of reactive oxygen species (ROS) have been associated with aging and its related pathological conditions. Recently, dietary antioxidants have gained significant attention as potential preventive and therapeutic agents against ROS-generated aging and pathological conditions. We previously demonstrated that food-derived antioxidants prevented intracellular oxidative stress under proteasome inhibition conditions, which was attributed to mitochondrial dysfunction and ROS generation, followed by cell death. Here, we further screened dietary antioxidants for their activity as redox modulators by visualization of the redox state using Redoxfluor, a fluorescent protein redox probe. Direct alleviation of ROS by antioxidants, but not induction of antioxidative enzymes, prevented mitochondria-mediated intracellular oxidation. The effective antioxidants scavenged mitochondrial ROS and suppressed cell death. Our study indicates that redox visualization under mitochondria-mediated oxidative stress is useful for screening potential antioxidants to counteract mitochondrial dysfunction, which has been implicated in aging and the pathogenesis of aging-related diseases. Direct alleviation of mitochondrial impairment-producing ROS by dietary antioxidants maintained intracellular redox state and improved cell viability.
Discovery of potential phytochemicals as inhibitors of TcdB, a major virulence factors of Clostridioides difficile
Creators: name: Alamri, Mubarak A.
name: Tariq, Muhammad Hamza
name: Qamar, Muhammad Tahir ul
name: Alabbas, Alhumaidi B.
name: Alqahtani, Safar M.
name: Ahmad, Sajjad
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Clostridioides difficile is a gram-positive bacterium which is associated with different gastrointestinal related infections, and the numbers of cases related to it are continuously increasing in the past few years. Owing to high prevalence and development of resistance towards available antibiotics, it is required to develop new therapeutics to combat C. difficile infection. The current study was aimed to identify novel phytochemicals that could bind and inhibits the TcdB, an exotoxin which is required for the pathogenesis of bacteria, and hence can be considered as the future drug candidates against C. difficile. ∼2500 therapeutically important phyto-compounds were docked against the active sites of TcdB protein by using AutoDock-Vina software. The interactions between the ligands and the binding site of the top five docked complexes, based on the docking scores, were further elucidated by Molecular Dynamics Simulations of 500 ns, Molecular Mechanics Energies combined with the Poisson–Boltzmann and Surface Area (MMPBSA) or Generalized Born and Surface Area (MMGBSA), and WaterSwap Analysis. Findings of molecular docking suggested that natural compounds A183, A704, A1528, A2083, and A2129 with distinct chemical scaffolds are best docked in the binding site of TcdB and their bonding remained stable throughout the simulation studies of 500 ns. Compounds A2129 and A704 can be considered as prospective drug candidates against Clostridioides difficile, however, further wet lab experiments are needed to confirm our study. Communicated by Ramaswamy H. Sarma
Characterisation and substrate binding modes of exopolygalacturonase PGQ1 from Saccharobesus litoralis
Creators: name: Azami, Nor Azura
name: Lian, Melissa Qianyue
name: Furusawa, Go
name: Teh, Aik-Hong
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Among the enzymes required for the efficient utilisation of pectin is polygalacturonase. Saccharobesus litoralis harbours two polygalacturonases belonging to glycoside hydrolase family 28 (GH28). One of them, PGQ1, cleaved polygalacturonate exolytically at the non-reducing end into monomeric units. It was most active at 60 °C and pH 8, with Km and kcat values of 2.3 mg/ml and 6.4 s−1 respectively. Its homology model of a right-handed parallel β-helix core consisted of Asp297 as the general acid and either Asp276 or Asp298 as the general base. By inferring the substrate binding modes at the −1 and +1 subsites from known crystal structures, a hexagalacturonate could be docked into the highly electropositive binding cleft. Interestingly, while no residues were present in the vicinity to make up the +2 and +4 subsites, Arg361 and Arg430 could readily bind to the carboxyl groups of the galacturonates at the +3 and +5 subsites respectively. Structural comparison suggested that this binding pattern with missing subsites might be unique to closely related exopolygalacturonases. As S. litoralis grew much more slowly on extracellular galacturonate due to the lack of a transporter for the monosaccharide, PGQ1 probably functioned in the periplasm to help degrade oligopectates completely. Communicated by Ramaswamy H. Sarma
Cow-calf Producers' Willingness to Pay for Bulls Resistant to Horn Flies, Haematobia irritans (L.) (Diptera: Muscidae)
Creators: name: Griffith, Andrew P.
name: McKay, Lettie
name: DeLong, Karen L.
name: Fryxell, R.T. Trout
name: Schexnayder, Susan
name: Taylor, David B.
name: Olafson, Pia
name: Griffith, Andrew P.
name: McKay, Lettie
name: DeLong, Karen L.
name: Fryxell, R.T. Trout
name: Schexnayder, Susan
name: Taylor, David B.
name: Olafson, Pia
Publisher: name: Unknown
Year: 2019
Subjects: subject: Farm Management
subject: Financial Economics
subject: Livestock Production/Industries
subject: Risk and Uncertainty
subject: Cow-calf
subject: producers
subject: willingness
subject: pay
subject: bulls
subject: resistant
subject: horn
subject: flies
subject: haematobia
subject: irritans
subject: diptera
subject: muscidae

description: In this publication, we report the survey results of cow-calf producers in Tennessee and Texas regarding their willingness to adopt a hypothetical HFR bull into their herds. This publication is adapted from McKay et al. (2019). In reporting these results, the objective is to inform cow-calf producers and seed stock producers of the factors that influence a producer’s decision to adopt a HFR bull. Thus, seedstock producers can use this information to determine if it is worth breeding for the HFR characteristic, while commercial cow-calf producers can use the information to make informed purchasing decisions, if the trait becomes available.