cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Lysozyme stability in various deep eutectic solvents using molecular dynamics simulations
Creators: name: Hebbar, Akshatha
name: Dey, Poulumi
name: Vatti, Anoop Kishore
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: The ability of neat deep eutectic solvents (DESs) to influence protein structure and function has gained considerable interest due to the unstable nature of enzymes or therapeutic proteins, which are often exposed to thermal, chemical, or mechanical stresses when handled at an industrial scale. In this study, we simulated a model globular protein, lysozyme, in water and six choline chloride-based DES using molecular dynamics simulations, to investigate the structural changes in various solvent environments, giving insights into the overall stability of lysozyme. Root mean square deviation (RMSD) and root mean square fluctuations (RMSF) of the C-α backbone indicated that most DESs induced a less flexible and rigid lysozyme structure compared to water. The radius of gyration and end-to-end distance calculations pointed towards higher structural compactness in reline and levuline, while the structure of lysozyme considerably expanded in oxaline. Protein-solvent interactions were further analysed by hydrogen bonding interactions and radial distribution functions (RDF), which indicated a higher degree of lysozyme-hydrogen bond donor (HBD) interactions compared to lysozyme-choline hydrogen bonding. Surface area analysis revealed an overall % increase in total positive, negative, donor, and acceptor surface areas in malicine and oxaline compared to water and other DESs, indicating the exposure of a larger number of residues to interactions with the solvent. Reline, levuline, and polyol-based DESs comparatively stabilized lysozyme, even though changes in the secondary/tertiary structures were observed. Communicated by Ramaswamy H. Sarma
Molophilus Curtis 1833
Creators: name: Billingham, Zacariah D.
name: Theischinger, Gunther
name: Levesque-Beaudin, Valerie
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Limoniidae
Molophilus

description: Genus Molophilus Curtis, 1833
Type species: Molophilus brevipennis Curtis, 1833, by original designation.
Diagnosis. Rostrum short, little developed; meron between mesocoxa and metacoxa extensive, seen from lateral aspect larger than mesocoxa; setae of legs simple; R l longer than 2/3 wing length; Rs ending in cell r 3; R 2+3 and R 4+5 distinct; R 5 not fused with M 1+2; r-m present; CuA 2 and A l not fused distally; a 2 long and wide (modified from Theischinger 1992).
The genus Molophilus includes over 1,000 species, present on all continents except Antarctica. Their diversity is greatest in the Australasian region, with 464 species occurring across Australia, New Caledonia, New Zealand, Papua New Guinea and West Papua (Oosterbroek 2023). Australia boasts more species of Molophilus than any other country or continent with 325 species recorded, including the species newly described here. Except for a single species, M. (Molophilus) flavonotatus Skuse, 1890, which is also known from New Zealand, the Australian species of Molophilus are all endemic.
Theischinger (1992) undertook a comprehensive review of the Australian Molophilus, describing many new species and providing a key to the subgenera and species groups. Following Theischinger’s review additional new species have been described over numerous works (Billingham & Theischinger 2018a, 2018b, 2019a, 2019b; Theischinger 1994, 1996a, 1999, 2000, 2012, 2017).
Molophilus is readily distinguished from other Australian Limoniid genera using the key provided in Theischinger (1996b).
description: Published as part of Billingham, Zacariah D., Theischinger, Gunther & Levesque-Beaudin, Valerie, 2023, Two new species of crane fly (Diptera: Limoniidae) from Tasmania, Australia, pp. 77-83 in Zootaxa 5256 (1) on page 80, DOI: 10.11646/zootaxa.5256.1.5, http://zenodo.org/record/7752370
Development of Safety in Structural Standards
Creators: name: Proske, Dirk
Publisher: name: Trinity College Dublin
Year: 2023

description: Nowadays, the required safety of structures is achieved through computational verifications and qualitative requirements for the building materials and the construction processes. Both the computational verifications and the qualitative requirements are shaped by increasingly specific scientific investigations and by political framework conditions. The target values of the required safety are largely developed by models focused on individual limit states, although individual collapses have an impact on the standards. An examination of safety across the entire stock of structures has not yet been carried out. In this paper, the safety of the stock of structures is determined from the ratio of the median calculated failure probabilities of different calculations and the median observed collapse frequencies over all structures. The ratio shows the absolute safety, i.e., the sum of safety from computational verifications and qualitative requirements. This allows an assessment of the quality of research and standard-ization work.
Positional difference and Frequency (PdF) based alignment-free technique for genome sequence comparison
Creators: name: Dey, Sudeshna
name: Ghosh, Papri
name: Das, Subhram
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: In the field of computational biology, genome sequence comparison among different species is essential and has applications in both the research and scientific fields. Owing to the lengthy processing time and large number of data sets, the alignment-based approaches are unsuitable and ineffective. Therefore, alignment-free techniques have obtained popularity for acquiring proper sequence clustering and evolutionary relationship among species. In this paper, a complete bipartite graph based Positional difference and Frequency (PdF) vector descriptor is introduced. Positional difference and Frequency, two parameters, are applied to the genome sequence to create a 16- dimensional vector descriptor using the di-nucleotide representation of genome sequence. Subsequently, a distance matrix is calculated to construct the phylogenetic trees for different data sets of mammals and viruses. The achieved outcomes are compared with the phylogenetic trees of the earlier methods viz. the FFP method, the ClustalW method, the MEV method, the PCNV method and the FIS method. In most instances, the proposed method produces more precise outcomes than the preceding techniques and has potential for genome sequence comparison on both the equal and unequal length of data-sets. Communicated by Ramaswamy H. Sarma
Computational identification and exploration of novel FGFR tyrosine kinase inhibitors for the treatment of cholangiocarcinoma
Creators: name: Kaur, Amanpreet
name: Mandal, Debasish
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer

description: Tyrosine kinase inhibitors are a specific drug class revolutionizing cancer treatment. FGFR (Fibroblast Growth Factor Receptor) is a member of the receptor tyrosine kinase family that has been involved in various alterations which have been increasingly recognized as critical molecular drivers in cholangiocarcinoma, a malignant tumor originating from bile duct epithelial cells. The paper focuses on stepwise computational investigations for the discovery of novel inhibitors of FGFR using pharmacophore modeling, virtual screening, docking, ADMET analysis, molecular dynamics, and knowledge-based structure-activity relationship. To begin with, we have considered a library of 120314868 compounds from the ZINC 15 database through pharmacophore modeling, which was narrowed down to 110 having binding affinity >−8.0 kcal mol−1. The 110 compounds were analyzed using virtual screening and compared with the FDA-approved drug pemigatinib, which provided the 34 hits with binding affinities >−6.5 kcal mol−1. Finally, the top 4 hits were considered for docking, and ADMET property analysis for drug-likeness. MD and MM-GBSA analysis were performed to predict the binding free energy of these chemicals and determine their stability. To gain insight into the structure and binding interactions of these compounds, knowledge-based SAR analyses were performed using their electrostatic potential maps computed with DFT. Several techniques were employed to build improved inhibitors based on these SAR, and they were then analyzed utilizing ADMET, MD studies, and MM-GBSA analyses. Finally, the results suggested that the identified four compounds and developed inhibitors from this current work can be employed effectively as prospective FGFR inhibitors for treating Cholangiocarcinoma. Communicated by Ramaswamy H. Sarma
Stigmaporus centralasiaticus Wolf 1990
Creators: name: Loktionov, Valery M.
name: Lelej, Arkady S.
name: Mokrousov, Mikhail V.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Pompilidae
Stigmaporus
Stigmaporus centralasiaticus

description: Stigmaporus centralasiaticus (Wolf, 1990)
(Figs 1, 30, 31)
Gonaporus centralasiaticus Wolf, 1990: 623 (key), 631 (description), ♀ (holotype, ♀, "Palu-Pass, centr. Asien, Zugmayer 1906",?USSR (deposited in R. Wahis coll., Gembloux, Belgium).
Gonaporus (Stigmaporus) centralasiaticus: S. Zonstein 2001: 142, 143, ♀ (Central Asia?). Stigmaporus centralasiaticus: I. Zonstein & Wahis 2015: 496.
Diagnosis. Female. Fore wing: distance between 2rs-m and inner margin of dark apical spot longer than maximum width of cell 1Rs (Fig. 30). Male. Unknown.
Distribution. China (Xinjiang) (Fig. 1).
Remarks. The holotype of Gonaporus centralasiaticus Wolf has been collected by Erich Zugmayer in Chinese Turkestan (Xinjiang) at the Pulu [Polu], elevation 2650 m, 180 km south-east of Hotan. E. Zugmayer collected the insects here at 11–15.VI.1906 (Zugmayer 1908, Parrot 1909).
description: Published as part of Loktionov, Valery M., Lelej, Arkady S. & Mokrousov, Mikhail V., 2016, Review of the genus Stigmaporus S. Zonstein, 2001 (Hymenoptera: Pompilidae), with description of new species, pp. 107-114 in Zootaxa 4126 (1) on page 109, DOI: 10.11646/zootaxa.4126.1.5, http://zenodo.org/record/265852
Megachile (Carinula) silverlocki Meade-Waldo 1913
Creators: name: Nkulu, Alain Tshibungu
name: Pauly, Alain
name: Dorchin, Achik
name: Vereecken, Nicolas J.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Megachilidae
Megachile
Megachile silverlocki

description: Megachile (Carinula) silverlocki Meade-Waldo, 1913
Chalicodoma (Carinella) silverlocki (Meade-Waldo, 1913)
Material. Cabinet 110, Drawer 25 (8 ♀ and 2 ♂). D.R. CONGO. Paratypes — Haut-Lomami • 1 ♂; Bukama; -9.20, 24.78; 10 Jun. 1911; Dr. M. Bequaert leg.; RMCA • 1 ♀; ibid; 16 Apr. 1911; Dr. J. Bequaert leg.; RMCA • 2 ♀; ibid; 21 Apr. 1911; Dr. J. Bequaert leg.; RMCA • 1 ♀; ibid; 23 Apr. 1911; Dr. J. Bequaert leg.; RMCA • 1 ♀; ibid; 7 Jul. 1911; Dr. J. Bequaert leg.; RMCA. • 1 ♀; Bukama; -9.20, 24.78; 12 Sep. 1911; Dr. J. Bequaert leg.; RMCA • 1 ♂; ibid; 12 Sep. 1911; Dr. J. Bequaert leg.; RMCA • 2 ♀; ibid; 4 sep. 1911; Dr. J. Bequaert leg.; RMCA.
description: Published as part of Nkulu, Alain Tshibungu, Pauly, Alain, Dorchin, Achik & Vereecken, Nicolas J., 2023, The Megachilidae (Hymenoptera, Apoidea, Apiformes) of the Democratic Republic of Congo curated at the Royal Museum for Central Africa (RMCA, Belgium), pp. 1-103 in Zootaxa 5392 (1) on page 45, DOI: 10.11646/zootaxa.5392.1.1, http://zenodo.org/record/10435063
Stigmaporus lystracantha Wolf 1988
Creators: name: Loktionov, Valery M.
name: Lelej, Arkady S.
name: Mokrousov, Mikhail V.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Pompilidae
Stigmaporus
Stigmaporus lystracantha

description: Stigmaporus lystracantha (Wolf, 1988)
(Figs 1, 24, 25)
Telostegus lystracantha Wolf, 1988: 236 (description), ♀ (holotype, ♀, "Schasenen [Shahsenem], sev. Kara-Kum, E. Arens, 5– 6.VI.1953 " [Altyn asyp, North Karakumy, Turkmenistan], [ZISP]; Wolf 2005: 1752, 1757, ♀ Ƌ (South-East Kazakhstan, Mongolia).
Gonaporus (Stigmaporus) lystracantha: S. Zonstein 2001: 142 –144, ♀ Ƌ (Turkmenistan). Stigmaporus lystracantha: I. Zonstein & Wahis 2015: 459, 462, 463, 496, ♀.
Diagnosis. Female and male. Abscissa Rs1 of hind wing as long as, or slightly longer than rs-m (Fig. 25). Distribution. Turkmenistan, South-East Kazakhstan, Mongolia (Ömnögovi) (Fig. 1).
description: Published as part of Loktionov, Valery M., Lelej, Arkady S. & Mokrousov, Mikhail V., 2016, Review of the genus Stigmaporus S. Zonstein, 2001 (Hymenoptera: Pompilidae), with description of new species, pp. 107-114 in Zootaxa 4126 (1) on page 109, DOI: 10.11646/zootaxa.4126.1.5, http://zenodo.org/record/265852
Stigmaporus wolfi S. Zonstein 2001
Creators: name: Loktionov, Valery M.
name: Lelej, Arkady S.
name: Mokrousov, Mikhail V.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Pompilidae
Stigmaporus
Stigmaporus wolfi

description: Stigmaporus wolfi (S. Zonstein, 2001)
(Figs 1, 21–23, 26–29, 34, 35)
Gonaporus (Stigmaporus) wolfi S. Zonstein, 2001: 143 (key, description), ♀ Ƌ (holotype, ♀, "[well] Orto-Kuju., tz.[central] Karakumy, E. Arens, 26.V. [1]953" [Turkmenistan], [ZISB] (Turkmenistan, Uzbekistan, South-East Kazakhstan, West Mongolia).
Stigmaporus wolfi: I. Zonstein & Wahis 2015: 462 –464, 496, ♀, Ƌ.
Diagnosis. Female and male. Abscissa Rs1 of hind wing shorter than vein rs-m (Figs 27, 29) (♀ ♂). Marginal cell of fore wing (along wing margin) noticeably longer than pterostigma (♀ ♂); distance between 2rs-m and inner margin of dark apical spot less than maximum width of cell 1Rs (Figs 26, 28) (♀ ♂). Spines of tarsal comb strongly broadened preapically, including preapical spine of protarsomere 4 which flattened and distinctly broadened (Fig. 34) (♀). Apical margin of hypopygium broadly oval (Fig. 22) (♂). Paramere of genitalia basally with short bristles (Fig. 21) (♂).
Distribution. Uzbekistan, Turkmenistan, South-East Kazakhstan and West Mongolia (Fig. 1).
description: Published as part of Loktionov, Valery M., Lelej, Arkady S. & Mokrousov, Mikhail V., 2016, Review of the genus Stigmaporus S. Zonstein, 2001 (Hymenoptera: Pompilidae), with description of new species, pp. 107-114 in Zootaxa 4126 (1) on page 109, DOI: 10.11646/zootaxa.4126.1.5, http://zenodo.org/record/265852
Theoretical aspects of the adsorption of normal and modified base pairs of DNA on graphene models toward DNA sequencing
Creators: name: Radhika, R.
name: Shankar, R.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified

description: A theoretical understanding of the adsorption of DNA base pairs (GC, AT, CAF-T and CAF-C) on the graphene models (Gr, SiGr and SiGr-COOH) is investigated. Among the complexes, SiGr-COOH_AT is found to have the highest adsorption energies of −202.83 kcal/mol. The strong adsorption between DNA base pairs and the SiGr-COOH model leads to concomitant charge transfer responsible for the stability of the corresponding models and is verified with NBO analysis. AIM analysis discloses the high orbital overlap that signifies the strong interaction. Closed-shell interactions are observed through the positive values of total electron density, and it is also observed that Si-O(N) interaction has both covalent and electrostatic characteristics. This is the first theoretical attempt to investigate the adsorption of DNA base pairs on SiGr-COOH, which is more favourable than other models and may call for further experimental studies, which is crucial in developing new bio-sensors. Communicated by Ramaswamy H. Sarma
Computational study on natural molecules targeting β-ketoacyl reductase domain of fatty acid synthase for the identification of selective inhibitors
Creators: name: Soukya, P. S. Lakshmi
name: Begum, A. Sajeli
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: Fatty acid synthase (FASN) enzyme is a lipid metabolism protein that provides the essential nutrients to cancer cells through de novo lipogenesis. Also, it plays a key role in other disease conditions, including obesity and inflammation. Hence, targeting the β-ketoacyl reductase (KR) domain of FASN protein, an in-silico study was performed on some selective bioactive natural molecules following a repurposing strategy to identify FASN inhibitors. A molecular docking study followed by Absorption, Distribution, Metabolism and Excretion (ADME) predictions, binding free energy calculations, and molecular dynamics (MD) simulations were performed against FASN protein (PDB ID:6NNA) using Schrodinger Drug Discovery Software. Compounds rutin, trans-chlorogenic acid, norbergenin, myricetin, quercetin, physalolactone, quercetin-3-O-galactoside, kaempferol, asperulosidic acid, luteolin, curcumin, 12-deoxywithastramonolide, pedunculoside, hernandifoline, and withafastuosin E were identified as hits, presenting better docking scores (–16.2, −14.1, −12.3, −12.1, −12.0, −11.3, −10.3, −9.8, −9.3, −9.2, −9.1, −8.5, −8.4, −8.3, –7.9, respectively) and hydrogen bond interactions with Ser 2021 and Tyr 2034 amino acids of the KR domain of FASN. The MD simulations study of top five hits in complex with protein 6NNA uncovered the significant interactions leading to the stabilization of ligand with Root Mean Square Deviation (RMSD) below 5.00 Å and the stability was further validated by evaluating the root mean square fluctuation, solvent accessible surface area, and radius of gyration graphs. Also, the FASN inhibition effect of top four hits (50 µM) was >50% when corroborated using High Performance Liquid Chromatography HPLC-based estimation of palmitic acid in MCF-7 cells. Thus rutin, trans-chlorogenic acid, norbergenin, and myricetin are proposed as prospective FASN inhibitory leads. Overall, the results provided useful modifications in pharmacophoric features that could improve the inhibitory effect. Communicated by Ramaswamy H. Sarma
Evaluating The Extent of Bio-Polyester Polymerization in Solid Wood by Thermogravimetric Analysis
Creators: name: Noël, Marion
name: Grigsby, Warren J.
name: Volkmer, Thomas
Publisher: name: Taylor & Francis
Year: 2015

description: In this study, the thermogravimetric analysis (TGA) technique has been applied to determine the extent of in situ polymerization achievable in solid wood on treating with bio-polyester oligomers. Low-molecular-weight oligomers of poly(lactic acid) (PLA), poly(glycolic acid) (PGA), poly(butylene succinate) (PBS), and poly(butylene adipate) (PBA) were impregnated and then thermally polymerized within solid wood to enhance the physical properties of wood. TGA revealed a similar degree of oligomer polymerization was achieved either with pure oligomers or within the wood structure. The influence of relatively acidic treatments, such as low-molecular-weight PGA oligomers, was observed to lead to degradation of the hemicellulose wood component. Polymerization of PLA and PGA oligomer treatments which penetrate the wood cell wall gave relatively lower wood thermal stability. Treatment and polymerization of lumen filling PBS and PBA oligomers contributed to increased wood thermal stability
Could fall armyworm, Spodoptera frugiperda (J. E. Smith) invasion in Africa contribute to the displacement of cereal stemborers in maize and sorghum cropping systems
Creators: name: Hailu, Girma
name: Niassy, Saliou
name: Bässler, Timon
name: Ochatum, Nathan
name: Studer, Christoph
name: Salifu, Daisy
name: Agbodzavu, Mawufe K.
name: Khan, Zeyaur R.
name: Midega, Charles
name: Subramanian, Sevgan
Publisher: name: Springer
Year: 2021
Subjects: Invasiveness.Displacement.Pest.Competition.Stem borer.Fall armywom

description: The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), which has recently invaded the African continent, has become a new threat to cereal production. Being an invasive pest with certain competitive advantages, the impact of FAW on other lepidopteran pests is unclear. This study assessed the infestation of FAW and cereal stemborers on maize and sorghum under mono-cropped systems that are adjacently placed in five districts in Uganda. Data on maize and sorghum infestation cereal stemborers and FAW was collected at 6, 9 and 16 weeks after planting (WAP), to determine intensity and severity. Cereal stemborer infestations on maize at 6, 9 and 16 WAP were only 36.7%, 48.2% and 24.0%, respectively, which was significantly lower than the infestations on sorghum, at 55.5%, 53.2%, 64.0%, respectively. On the contrary, the infestations of FAW on maize at 6, 9 and 16 WAP were 89.5%, 84.7% and 86.0%, respectively, while on sorghum they were 51.0%, 56.5% and 47.0, respectively. The severity of stemborers on sorghum was statistically higher than on maize, whereas the damage severity of FAW was generally higher on maize than on sorghum. Intensity of damage and cavity length due to stemborer on sorghum was higher than on maize. Historical records showed that in maize stemborer infestation could reach 60%. This infestation started significantly declining in 2016, suggesting an early arrival of FAW in Uganda. The present study indicates a possible displacement of stemborer from maize onto sorghum. Any Integrated Pest Management (IPM) package should consider managing FAW and stemborer together in both maize and other cereal hosts.
Inhibitor screening for volume-sensitive LRRC8A chloride channel
Creators: name: Liu, Chao
name: Cui, Wenqiang
name: Zhu, Kongfu
name: Yuan, Shuguang
name: Sun, Liang
name: Liang, Yujie
name: Lu, Jianping
name: Li, Da
name: Deng, Zhiqin
name: Duan, Li
name: Zhang, Weiming
name: Yu, Xiaohai
name: Wang, Daping
name: Zhang, Huawei
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
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: Leucine-rich repeat-containing protein 8 A (LRRC8A) protein is a critical member of volume-regulated anion channels. It plays a critical roles in the regulation of cellular volume and involves in the development of diseases like osteoarthritis. Screening of lead compounds to modulate its function may provide potential therapeutics of related diseases. Here, we employ virtual screening techniques and molecular dynamics (MD) simulation to screen potential inhibitors against LRRC8A. LRRC8A was regarded as the drug target to investigate potential compounds from the ZINC15 database via molecular docking. The final compound was selected among the top 10 Autodock Vina score (–8.8 Kcal/mol) with the ZINC ID ZINC000018195627 after druggability prediction. The docked complex from the virtual screening was subjected to MD simulation to analyze the stability of the LRRC8A protein–ligand complex, with parameters including root mean square deviation, root mean square fluctuation and radius of gyration. Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) method was further employed to predict the binding free energies from MD simulation trajectory. Our study provides insightful analysis for the potential compound to modulate LRRC8A and lay the foundation of therapeutics development against osteoarthritis. Communicated by Ramaswamy H. Sarma
α-Amylase and mycobacterium-TB H37Rv antagonistic efficacy of novel pyrazole-coumarin hybrids: an in vitro and in silico investigation
Creators: name: Kanjariya, Dilip C.
name: Naik, Hem N.
name: Sherashiya, Meet J.
name: Naliapara, Yogesh T.
name: Ahmad, Iqrar
name: Patel, Harun
name: Rajani, Dhanji
name: Jauhari, Smita
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: The present investigation of minutiae to acquire structural information of the novel pyrazole-coumarin hybrids (PC1-PC10) synthesized using ultrasound methods and characterized using different spectroscopic techniques: mass, 1H-NMR, 13 C-NMR and IR spectroscopy, and theoretically explored using the DFT approach with a B3LYP/6–311G (d, p) basis set, and there in vitro, antagonistic efficacy against α-amylase and mycobacterium-TB H37Rv are described in this article. Pyrazole-coumarin hybrids (PC1-PC10) showed α-amylase inhibition ranging from IC50 (0.32–0.58 mM) when compared with acarbose (IC50 = 0.34 mM). Similarly, Mycobacterium-TB H37Rv strain inhibition screening showed MIC values ranging from 62.5 to 1000 µg/mL when compared with rifampicin and isoniazid MIC = 0.25 and 0.20 µg/mL, respectively. Molecular docking and MD simulation studies were performed to determine the active sites and rationalize the activities of the active compounds. To investigate the binding conformation and dynamics responsible for their activity, the three most active compounds (PC1, PC3 and PC6) were docked into the porcine pancreatic α-amylase active site (PDB ID:1OSE), and mycobacterium-TB H37Rv active site (PDB ID: 4TZK). The binding interactions between PC1, PC3, and PC6 with α-amylase were like those responsible for inhibiting α-amylase by acarbose. Also, the mycobacterium-TB H37Rv inhibiting responsible residues were compared with standard isoniazid and rifampicin. Communicated by Ramaswamy H. Sarma
Modeling and monitoring the effects of three partly conserved Ile residues in the dimerization domain of a Mip-like virulence factor from Escherichia coli
Creators: name: Seal, Soham
name: Chakraborty, Tushar
name: Polley, Soumitra
name: Paul, Debarati
name: Banerjee, Nilanjan
name: Sinha, Debasmita
name: Dutta, Anindya
name: Chatterjee, Subhrangsu
name: Sau, Keya
name: Dastidar, Shubhra Ghosh
name: Sau, Subrata
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: FKBP22, an Escherichia coli-made peptidyl-prolyl cis-trans isomerase, has shown considerable homology with Mip-like virulence factors. While the C-terminal domain of this enzyme is used for executing catalytic function and binding inhibitor, the N-terminal domain is employed for its dimerization. To precisely determine the underlying factors of FKBP22 dimerization, its structural model, developed using a suitable template, was carefully inspected. The data show that the dimeric FKBP22, like dimeric Mip proteins, has a V-like shape. Further, it dimerizes using 40 amino acid residues including Ile 9, Ile 17, Ile 42, and Ile 65. All of the above Ile residues except Ile 9 are partly conserved in the Mip-like proteins. To confirm the roles of the partly conserved Ile residues, three FKBP22 mutants, constructed by substituting them with an Ala residue, were studied as well. The results together indicate that Ile 65 has little role in maintaining the dimeric state or enzymatic activity of FKBP22. Conversely, both Ile 17 and Ile 42 are essential for preserving the structure, enzymatic activity, and dimerization ability of FKBP22. Ile 42 in particular looks more essential to FKBP22. However, none of these two Ile residues is required for binding the cognate inhibitor. Additional computational studies also indicated the change of V-shape and the dimeric state of FKBP22 due to the Ala substitution at position 42. The ways Ile 17 and Ile 42 protect the structure, function, and dimerization of FKBP22 have been discussed at length. Communicated by Ramaswamy H. Sarma
Extraordinarius angusyoungi Rheims 2022, spec. nov.
Creators: name: Rheims, Cristina A.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Araneae
Sparassidae
Extraordinarius
Extraordinarius angusyoungi

description: Extraordinarius angusyoungi spec. nov.
Figs 17−23
Type material. Holotype: BRAZIL: Rio de Janeiro: ♀, Fazenda Ranchinho da Roça, Petrópolis [‑22.4500, ‑43.2000], 15−16 August 2001, Equipe Biota leg. (IBSP 43247).
Etymology. The species name honors Angus Young, lead guitarist, songwriter and co-founder of the Australian rock band AC/DC. He is best known for his stage schoolboy uniform outfits and energetic performances; name in genitive case.
Diagnosis. Females of E. angusyoungi spec. nov. resemble those of E. rickalleni (Rheims 2019: figs 62−64) and E. alicecooperi spec. nov. (Figs 14−16) by the epigyne with MS lacking anterior scape, but are distinguished by the rectangular shape of the MS (inverted T-shaped in E. alicecooperi spec. nov. and ovoid in E. rickalleni) and by the vulva with packed structures running almost parallel to each other (strongly converging towards each other in both other species) (Figs 21−23).
Description. Female (holotype): Prosoma brown; fovea very slightly darker than prosoma; eye borders black. Chelicerae brown. Legs and palps orange brown, lighter than prosoma. Labium and endites brown, distally pale brownish cream colored. Sternum orange brown with brown margins. Opisthosoma brownish gray; dorsally with brown pattern of irregular shaped marks on anterior half and laterally, and five median chevron-like marks down posterior half; ventrally with few scattered brown spots laterally and median U‑shaped line of muscle impressions. Spinnerets orange brown, distally yellowish brown (Figs 17−18). Total length 14.5. Prosoma 5.8 long, 5.0 wide. Opisthosoma 8.2 long, 5.0 wide. Eyes: diameters: 0.34, 0.30, 0.21, 0.30; interdistances: 0.35, 0.32, 0.58, 0.58, 0.25, 0.15. Legs (4213): I: 13.4 (4.0, 2.5, 3.3, 2.7, 0.9); II: 13.5 (4.2, 2.6, 3.2, 2.6, 0.9); III: 11.1 (3.5, 2.0, 2.4, 2.3, 0.9); IV: 14.3 (4.2, 1.9, 3.2, 3.8, 1.2). Epigyne: EF slightly wider than long; LL with lateral groves strongly diverging anteriorly; MS roughly one and a half times wider than long (Figs 19, 21). Vulva: double helix with 9−10 twists; FD antero‑laterad (Figs 20, 22−23).
Male: unknown.
Distribution. Only known from the type locality, in Rio de Janeiro, southeastern Brazil (Fig. 31).
description: Published as part of Rheims, Cristina A., 2022, New species and records of the genus Extraordinarius Rheims, 2019 (Araneae Sparassidae: Sparianthinae), pp. 190-200 in Zootaxa 5205 (2) on pages 195-196, DOI: 10.11646/zootaxa.5205.2.6, http://zenodo.org/record/7305871
Virtual screening and invitro evaluation of cyclooxygenase inhibitors from Tinospora cordifolia using the machine learning tool
Creators: name: Mathe, Amaze
name: Mulpuru, Viswajit
name: Katari, Sudheer Kumar
name: Karlapudi, Abraham Peele
name: T.C, Venkateswarulu
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Virology

description: Tinospora cordifolia has a variety of compounds, and some of these compounds may have anti-inflammatory and antioxidant properties. In the present study, we identified the compounds in the leaf extract of T. cordifolia through Gas Chromatography-Mass Spectrometry (GC-MS) analysis and found the various metabolites. The compounds are screened virtually using a machine learning model, followed by molecular docking and simulation study to identify top-hit compounds as cyclooxygenase (COX) inhibitors. The molecular docking revealed that the compound 7,9-Di-tert-butyl-1-oxaspiro (4,5) deca-6,9-diene-2,8-dione (CID:545303) exhibited the lowest binding energies of −7.1 and −6.8 kcal/mol against COX 1 and COX 2 respectively. The interactions are favored by hydrogen bonding and hydrophobic interaction inside the binding pocket. The 100 ns MD simulation study for these compounds was performed to know the stability and found the RMSD around 2 Å and around 1.0 Å with minimal fluctuations indicating a stable complex throughout the simulation of 100 ns. Based on these findings, we proposed 7,9-Di-tertbutyl- 1-oxaspiro (4,5) deca-6,9-diene-2,8-dione could be used as a dual inhibitor of COX enzymes and a drug-like molecule for treating inflammation after evaluation of their biological properties. The methanolic extract of T. cordifolia was subjected to in vitro DPPH, ABTS, nitric oxide, anti-microbial, COX, and LOX inhibition activity. The results exhibited possible positive effects against the above activities. Communicated by Ramaswamy H. Sarma
Extraordinarius klausmeinei Rheims 2019, sp. nov.
Creators: name: Rheims, Cristina A.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Araneae
Sparassidae
Extraordinarius
Extraordinarius klausmeinei

description: Extraordinarius klausmeinei sp. nov.
http://zoobank.org/ D25AB52B-FED7-4DE3-BEBC-9E7DF3231C3B
Figs 40–49, 65
Type material: Holotype: ♂ from Parque Estadual de Itaúnas (18º25’S, 39º42’W), Conceição da Barra, Espírito Santo, Brazil, 15 December 2002 – 6 March 2003, Equipe Biota leg. (IBSP 60005).
Etymology. The specific name honours Klaus Meine, German singer, songwriter, lead singer of the hard rock band Scorpions; name in genitive case.
Diagnosis. Males of E. klaumeinei sp. nov. resemble those of E. andrematosi sp. nov. by the triangular shape of the TBC in the male palps (Figs 43, 46). They are distinguished by the RTA distally flattened and almost straight in retrolateral view (Figs 44, 49) (bent at a 90º angle in E. andrematosi sp. nov.) and by the MA with a widened base (same width throughout in E. andrematosi sp. nov.) (Figs 43, 48–49). Females are unknown.
Description. Male (Holotype): Prosoma brown, darker at lateral margins; fovea slightly darker; eye borders black. Chelicerae brown. Endites pale brown, distally cream colored. Labium brown, with dark brown base. Sternum orange with pale brown margins. Legs and pedipalps brown, slightly lighter than prosoma. Opisthosoma cream colored; dorsally with brown pattern of spots on anterior half and chevron-like marks medially down posterior half; ventrally with few scattered brown spots. Spinnerets pale orange (Figs 40–41). Total length 10.3. Prosoma: 4.6 long, 3.9 wide. Opisthosoma: 5.5 long, 3.2 wide. Eye diameters: 0.34, 0.25, 0.20, 0.27; interdistances: 0.25, 0.12, 0.40, 0.35, 0.17, 0.08. Legs (4123): I: 13.4 (3.9, 2.3, 3.4, 3.0, 0.8); II: 13.3 (4.1, 2.4, 3.1, 2.9, 0.8); III: 10.8 (3.4, 1.7, 2.5, 2.5, 0.7); IV: 14.2 (4.4, 1.6, 3.2, 3.9, 1.1). Spination follows the generic pattern except femur III r1-0-0; tibiae I–II: v4-2 -2; tibia IV v2-2 -2; metatarsus I–II v2-1 r-0. Palp: VTA conical, retrolaterally displaced; RTA single, slightly over 3 times longer than wide, retrolatero-distad in ventral view; TBC slightly wider than long; MA 1.5 times longer than basal width, arising from tegulum at 5:30 o’clock position; E arising from tegulum at 7 o’clock position (Figs 42–49).
Female unknown.
Distribution. Only known from the type locality in Espírito Santo (Fig. 65).
description: Published as part of Rheims, Cristina A., 2019, Extraordinarius gen. nov., a new genus of Sparianthinae spiders (Araneae: Sparassidae) from southeastern Brazil, pp. 83-99 in Zootaxa 4674 (1) on pages 92-93, DOI: 10.11646/zootaxa.4674.1.4, http://zenodo.org/record/3458436
Design, syntheses, theoretical calculations, MM-GBSA, potential anti-cancer and enzyme activities of novel Schiff base compounds
Creators: name: Yalazan, Halise
name: Koç, Damla
name: Kose, Fadime Aydın
name: Fandaklı, Seda
name: Tüzün, Burak
name: Akgül, Muhammed İsmail
name: Sadeghian, Nastaran
name: Taslimi, Parham
name: Kantekin, Halit
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Virology

description: In this study, new Schiff base compounds (SB-F-OH, SB-Cl-OH and SB-Br-OH) were derived from chalcone-derived amine compounds containing halogen groups and 4-hydroxybenzaldehyde. Also, their phthalonitrile compounds (SB-F-CN, SB-Cl-CN and SB-Br-CN) have been synthesized. The structures of these compounds were elucidated by NMR, FT-IR and Mass spectroscopic methods. The quantum chemical parameters were calculated at B3LYP/6–31++g(d,p), HF/6–31++g(d,p) and M062X/6–31++g(d,p) levels. As the biological application of the synthesized compounds, (i) their inhibition properties of the synthesized compounds on Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE) metabolic enzymes were investigated, and their potential anticancer activities against neuroblastoma (NB; SH-SY5Y) and healthy fibroblast (NIH-3T3) cell lines were determined by in vitro assays. All compounds showed inhibition at nanomolar level with the Ki values in the range of 97.86 ± 30.51–516.82 ± 31.42 nM for AChE, 33.21 ± 4.45–78.50 ± 8.91 nM for BChE, respectively. It has been determined that all tested compounds have a remarkable cytotoxic effect against SH-SY5Y, and IC50 values were significantly lower than NIH-3T3 cells. The lowest IC50 value was observed in SB-Cl-OH (7.48 ± 0.86 µM) and SB-Cl-CN (7.31 ± 0.69 µM). The molecular docking of the molecules was also investigated using crystal structure of AChE enzyme protein (PDB ID: 4M0E), crystal structure of BChE protein (PDB ID: 6R6V) and SH-SY5Y cancer protein (PDB ID: 2F3F, 3PBL and 5WIV). The ADME properties of the compounds were investigated. MM/GBSA method is calculated binding free energy. Afterwards, ADME/T analysis was performed to examine the some properties of the molecules. Communicated by Ramaswamy H. Sarma
Synthesis, biological evaluation, and molecular docking study of xanthene-linked thiosemicarbazones as cholinesterase inhibitors
Creators: name: Naseem, Saira
name: Khan, Samra
name: Hussain, Safdar
name: Mirza, Muhammad Usman
name: Ashraf, Muhammad
name: Shafiq, Zahid
name: Trant, John F.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Neuroscience
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Information Systems not elsewhere classified

description: This study delineates the design and synthesis of a series of xanthene-based thiosemicarbazones that show low μM inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), crucial enzymes associated with, among others, Alzheimer’s Disease (AD) pathology. Despite FDA-approved AChE inhibitors being frontline treatments for AD, there remains a need for agents exhibiting improved efficacy and selectivity. Our synthesized series demonstrate meaningful inhibition against AChE (IC50 ranging from 4.2 to 62 μM). These compounds exhibit comparatively lower potency against BChE (IC50 values between 64 and 315 μM), showcasing a pronounced AChE selectivity compared to physostigmine. The selectivity index for the compounds between the two targets does vary between 0.02 and 0.75 highlighting that even minor structural differences can have drastic effects on protein interactions. Molecular docking insights further substantiated these observations, revealing the importance of the xanthene scaffold for AChE-binding and the aryl R2 moiety for BChE interactions. Notably, some compounds demonstrated dual enzyme targeting, emphasizing their interactions could be exploited for developing monotherapies against cholinesterase-associated neurodegenerative afflictions like AD. Collectively, these findings suggest that xanthene-based thiosemicarbazones are a promising and highly accessible scaffold that deserve further investigative exploration in the cholinesterase inhibitor therapeutic landscape. Communicated by Ramaswamy H. Sarma Xanthene-thiosemicarbazones with low μM inhibition can be prepared in two steps without chromatographic purification and show strong selectivity for acetylcholinesterase over butyrylcholinesterase. This selectivity can be rationalized using computational methods and could serve as preliminary hits for further development.
Synthesis, structural and X-ray analysis evaluations and computational studies of newly tetrahydroisoquinoline derivatives as potent against microsomal prostaglandin E synthase 1
Creators: name: Mohamed, Shaaban K.
name: Karthikeyan, Subramani
name: Khamies, Esraa
name: Ahsin, Atazaz
name: Bakhite, Etify
name: Marae, Islam S.
name: El-Emary, Talaat I.
name: Mague, Joel T.
name: Said, Awad I.
name: Al-Salahi, Rashad
name: Bakri, Youness El
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified

description: Tetrahydroisoquinolines (THIQs) are a significant class within the broad range of natural compounds known as isoquinoline alkaloids. Natural and manmade drugs based on THIQ have a variety of biological effects that protect against different infectious pathogens and neurological diseases. In this study, two new THIQ derivatives were synthesized and characterized using by X-ray crystallographic analysis. The performed Hirshfeld analysis shows the intermolecular interactions and reactive sites of compounds. The 2D fingerprints reveal dominants H···C interactions up to 8.8% in 3a while 43% H···H elemental interactions are observed in compound 3b. In studied compound 3a, the repulsion energies (k-rep) dominate the other energies where the highest amount of 63.8 kJ/mol is obtained whereas 3b has a significant contribution from E-dis to the total energy of the molecule from the energy framework study. Moreover, the density functional theory study reveals better thermodynamic and electronic stabilities. These compounds have reduced HOMO-LUMO gaps (EH-L) ranging from 3.66 to 3.60 eV, indicating their remarkable conductive and electronic properties. The significant reduction in EH-L also guarantees our synthesized compounds’ soft nature and reactivity. Our studied compound’s NBO charges and MEPs analysis show electron-rich sites and donor–acceptor mechanism. Our synthesized compounds have remarkable polarizability (αo) and hyperpolarizability (βo) values (446.23 − 1312.73 au), which indicates their optical and nonlinear optical properties. The density of states spectra further illustrates their notable structural-electronic properties and reduced band gaps. Based on structural activity relationship studies, we found that these tetrahydro-isoquinolines derivatives are potent against microsomal prostaglandin E synthase 1(MPGES1), the docking analysis shows that studied compounds have a good binding affinity with MPGES1, and further ADME/T analysis was carried out for both compounds. In addtion to this molecular dynamics, studies were performed to understand the binding stability of both compounds in protien complex system during 100 ns simulation. Communicated by Ramaswamy H. Sarma
Study of self-assembling properties of HBc-VLP derivatives aided by molecular dynamic simulations from a thermodynamic perspective
Creators: name: Luo, Hong
name: Ma, Yanyan
name: Ren, Ying
name: Li, Zhengjun
name: Sheng, Yanan
name: Wang, Yingli
name: Su, Zhiguo
name: Bi, Jingxiu
name: Zhang, Songping
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: Self-assembling protein nanoparticles showed promise for vaccine design due to efficient antigen presentations and safety. However, the unpredictable formations of epitopes-fused protein assemblies remain challenging in the upstream design. This study suggests employing molecular dynamic (MD) simulations to investigate the assembly properties of Hepatitis B core protein (HBc) from thermodynamic perspectives. Eight HBc derivatives were expressed in E. coli, with their self-assembly properties characterised by high-performance liquid chromatography and transmission electron microscopy. MD simulations on the dimers, based on AlphaFold-predicted 3D structures, analysed the derivative at the atomic level. Results revealed that HBc derivatives can form dissociative polymers or large multi-subunit structures due to assembly failures. The instability of the dimer in aqueous solvents or inappropriate intradimer distances could cause major assembly failures. Polar solvation energies played a vital role too in forming assemble-incompetent dimers. Importantly, our study demonstrated that MD simulations on dimers can provide preliminary predictions on the assembly properties of HBc derivatives, thus aiding vaccine design by lowering the risk of self-assembling failures in engineered proteins. Communicated by Ramaswamy H. Sarma
[Théâtrales l’association - Les lundis du théâtre]
Creators: name: Théâtrales L’association
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2024
Subjects: Théâtre
Conférence

description: Présentation de deux conférences proposées par ''Théâtrales l’association'' dans le cadre de ''Les lundis du théâtre'' : ''Le théâtre en exil : paroles d’auteurs'' avec Eduardo Manet parmi les intervenants le 18 janvier 1999, et ''Les nouvelles voix de l’écriture théâtrale à la radio'' le 15 février 1999.
description: Presentación de dos conferencias propuestas por ''Théâtrales l’association'' en el marco de ''Les lundis du théâtre'' (''Los lunes del teatro''): ''Le théâtre en exil : paroles d’auteurs'' (''El teatro en el exilio: letras de autores'') con Eduardo Manet entre los oradores el 18 de enero de 1999, y ''Les nouvelles voix de l’écriture théâtrale à la radio'' (''Las nuevas voces de la escritura teatral en la radio'') el 15 de febrero de 1999.
description: Source: EM-C1-1-1999-01-18
description: Source: Localisation de la ressource : Centre de Recherches Latino-Américaines (CRLA–Archivos, ITEM UMR8132). MSHS - Bât. A5, 1er étage 5 rue Théodore Lefebvre - TSA21103. 86073 Poitiers cedex 9.