Journal articles: 'Compound identification'

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Opialla, Tobias, Stefan Kempa, and Matthias Pietzke. "Towards a More Reliable Identification of Isomeric Metabolites Using Pattern Guided Retention Validation." Metabolites 10, no. 11 (November 12, 2020): 457. http://dx.doi.org/10.3390/metabo10110457.

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Reliable analyte identification is critical in metabolomics experiments to ensure proper interpretation of data. Due to chemical similarity of metabolites (as isobars and isomers) identification by mass spectrometry or chromatography alone can be difficult. Here we show that isomeric compounds are quite common in the metabolic space as given in common metabolite databases. Further, we show that retention information can shift dramatically between different experiments decreasing the value of external or even in-house compound databases. As a consequence the retention information in compound databases should be updated regularly, to allow a reliable identification. To do so we present a feasible and budget conscious method to guarantee updates of retention information on a regular basis using well designed compound mixtures. For this we combine compounds in “Ident-Mixes”, showing a way to distinctly identify chemically similar compounds through combinatorics and principle of exclusion. We illustrate the feasibility of this approach by comparing Gas chromatography (GC)–columns with identical properties from three different vendors and by creating a compound database from measuring these mixtures by Liquid chromatography–mass spectrometry (LC–MS). The results show the high influence of used materials on retention behavior and the ability of our approach to generate high quality identifications in a short time.

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Li, Hong Zheng, He Zhou, and Yao Hong Jin. "A Method for Identifying V+N Compound Nouns in Patent Machine Translation." Applied Mechanics and Materials 513-517 (February 2014): 4617–20. http://dx.doi.org/10.4028/www.scientific.net/amm.513-517.4617.

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In this paper, we introduced one kind of special compound noun in Chinese patent texts composed of verb and noun, and presented a rule-based method for Chinese-English patent Machine Translation (MT) to improve the identification of compound nouns, with the purpose of decreasing the possibilities that verbs may disturb the identification of core predicate verb. The system first tagged different weights on verbs then determined the properties of verbs and recognized the compounds according to the weights. We then conducted experiments with the method, which proved that the method could identify compound nouns efficiently.

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Sudirman, Sabri, Nurjanah Nurjanah, and Agoes Mardiono Jacoeb. "Identification of Antioxidant Compounds Structure Large-Leafed Mangrove Fruit." Jurnal Pengolahan Hasil Perikanan Indonesia 19, no. 2 (August 30, 2016): 94. http://dx.doi.org/10.17844/jphpi.v19i2.13452.

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Antioxidants are compounds that can inhibit or prevent the oxidation of the easily oxidized substrate. One of the plants as a potential source of bioactive compounds and antioxidant activity is large-leafed mangrove (Bruguiera gymnorrhiza). This plant is commonly found in the Pacific region of Southeast Asia, Ryukyu Islands, Micronesia and Polynesia (Samoa) to subtropical regions of Australia and has been used by the society. This study aimed to determine the bioactive compounds structure of large-leafed mangrove has the highest antioxidant activity. The compound structure prediction was done by Nuclear Magnetic Resonance (NMR). The compound structure in the selected antioxidant fractions are flavonol, glikosilfalvon and flavon. Those three compounds are flavonoid compound which has a great role as the one that has antioxidant activity in large-leafed mangrove fruit.

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Yang, Wenzhi, Guangjie Liang, Yang Sun, and Zhijin Gong. "Bioactive Secondary Metabolites from Marine Streptomyces griseorubens f8: Isolation, Identification and Biological Activity Assay." Journal of Marine Science and Engineering 9, no. 9 (September 7, 2021): 978. http://dx.doi.org/10.3390/jmse9090978.

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Marine actinomycetes are a potential source of a wide variety of bioactive natural products. Herein, four cyclic dipeptides, namely, cyclo(L-Val-L-Pro) (compound 1), cyclo(L-Pro-L-Leu) (compound 2), cyclo(L-Pro-L-Tyr) (compound 3) and cyclo(L-Pro-L-Phe) (compound 5), and an N-acetyltyramine (compound 4) were first isolated and identified as products of the marine Streptomyces griseorubens f8. Compounds 3 and 5 exhibit antibacterial activity against Staphylococcus aureus, Klebsiella aerogenes and Proteus vulgaris. The minimum inhibitory concentrations (MICs) against Staphylococcus aureus, Klebsiella aerogenes and Proteus vulgaris are 160 µg/mL, 100 µg/mL, 120 µg/mL for the compound 3 and 180 µg/mL, 130 µg/mL 150 µg/mL for the compound 5, respectively. In addition, compounds 1, 2, 3 and 5 was first found to have the ability to inhibit the invasion and migration of A549 cells (lung cancer cells), which exhibited the potentiality for these compounds to be used as novel anticancer drugs. This study provides a novel production strain for compounds 1, 2, 3 and 5, and four potential promising anticancer agents.

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Veijanen, A., E. Kolehmainen, R. Kauppinen, M. Lahtiperä, and J. Paasivirta. "Methods for the Identification of Tainting Terpenoids and other Compounds from Algae." Water Science and Technology 25, no. 2 (January 1, 1992): 165–70. http://dx.doi.org/10.2166/wst.1992.0048.

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Off-flavour compounds produced by algae in freshwater ecosystems were studied for their structure using integrated sensory and spectroscopic methods: mass spectrometry (MS), nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR). Both solvent extraction and thermal desorption were used to isolate and to introduce the compounds into gas chromatography/mass spectrometry (GC/MS) and gas chromatography/Fourier transform infrared (GC/FTIR) systems. Ten ng of a terpenoid compound gave a readable IR spectrum. For 1H NMR studies the compounds were collected directly into NMR solvent by preparative gas chromatography. About 5 µg of a monoterpenoid compound was needed for a reliable 1H NMR spectrum. The mass spectral data indicated that the series of odorous substances detected by GC were terpenoid hydrocarbons and a later eluting series of compounds were sesquiterpene alcohols. In addition, one compound with an intense off-odour (aromatic, nitrogen containing compound) and some tainting carboxylic acids (derived from a starch factory) were detected.

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Bowes, Scott, Dongyu Sun, Azita Kaffashan, Chenhui Zeng, Claudio Chuaqui, Xiaoping Hronowski, Alex Buko, Xin Zhang, and Serene Josiah. "Quality Assessment and Analysis of Biogen Idec Compound Library." Journal of Biomolecular Screening 11, no. 7 (September 14, 2006): 828–35. http://dx.doi.org/10.1177/1087057106290993.

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A subset of the compound repository for lead identification at Biogen Idec was characterized for its chemical stability over a 3-year period. Compounds were stored at 4 °C as 10 mM DMSO stocks, and a small subset of compounds was stored as lyophilized dry films. Compound integrity of 470 discrete compounds (Compound Set I) and 1917 combinatorial chemistry-derived compounds (Compound Set II) was evaluated by liquid chromatography/mass spectrometry from the time of acquisition into the library collection and after 3 years of storage. Loss of compound integrity over the 3 years of storage was observed across the 2 subsets tested. Of Compound Set I, 63% of samples retained > 80% purity, whereas 57% of samples from Compound Set II had purity greater than 60%. The stability of the lyophilized samples was superior to the samples stored as DMSO solution. Although storage at 4 °C as DMSO solution was adequate for the majority of compounds, the authors observed and quantified the level of degradation within the compound collection. Their study provides general insight into compound storage and selection of library subsets for future lead identification activities.

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Yoneyama-Hirozane, Mariko, Kohei Deguchi, Takeshi Hirakawa, Tsuyoshi Ishii, Tomoyuki Odani, Junji Matsui, Yoshihide Nakano, et al. "Identification and Characterization of a New Series of Ghrelin O-Acyl Transferase Inhibitors." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 2 (August 28, 2017): 154–63. http://dx.doi.org/10.1177/2472555217727097.

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Ghrelin O-acyl transferase (GOAT; MBOAT4) catalyzes O-acylation at serine-3 of des-acyl ghrelin. Acyl ghrelin is secreted by stomach X/A-like cells and plays a role in appetite and metabolism. Therefore, GOAT has been expected to be a novel antiobesity target because it is responsible for acyl ghrelin production. Here, we report homogeneous time-resolved fluorescence (HTRF) and enzyme-linked immunosorbent assay (ELISA) methods utilizing human GOAT-expressing microsomes as a novel high-throughput assay system for the discovery of hit compounds and optimization of lead compounds. Hit compounds exemplified by compound A (2-[(2,4-dichlorobenzyl)sulfanyl]-1,3-benzoxazole-5-carboxylic acid) were identified by high-throughput screening using the HTRF assay and confirmed to have GOAT inhibitory activity using the ELISA. Based on the hit compound information, the novel lead compound (compound B, (4-chloro-6-{[2-methyl-6-(trifluoromethyl)pyridin-3-yl]methoxy}-1-benzothiophen-3-yl)acetic acid) was synthesized and exhibited potent GOAT inhibition with oral bioavailability. Both the hit compound and lead compound showed octanoyl-CoA competitive inhibitory activity. Moreover, these two compounds decreased acyl ghrelin production in the stomach of mice after their oral administration. These novel findings demonstrate that GOAT is a druggable target, and its inhibitors are promising antiobesity drugs.

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Chira, Kleopatra, Laura Anguellu, Gregory Da Costa, Tristan Richard, Eric Pedrot, Michael Jourdes, and Pierre-Louis Teissedre. "New C-Glycosidic Ellagitannins Formed upon Oak Wood Toasting, Identification and Sensory Evaluation." Foods 9, no. 10 (October 16, 2020): 1477. http://dx.doi.org/10.3390/foods9101477.

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In the courses of studies on ellagitannin changes during oak wood toasting, two C-glycosidic ellagitannins were isolated from the french oak wood for the first time. These two compounds exhibited [M−H]− ion peak at m/z 1055.0631 (compound A) and at m/z 1011.0756 (compound B). A compound is named Castacrenin E and is produced by Castacrenin D oxidation. Castacrenin D is a vescalagin with an additional aromating ring to the C-1 through a C-C bond. These compounds are not only found under laboratory conditions but also in commercial oak wood representing different toasting methods and sizes. Their levels are conditioned by oak wood dimensions and toasting degree. The wood pieces with the smallest size present almost two times more compounds A and B. Moreover, the compound B is the only compound to be present in medium toasting temperatures of the smallest wood pieces. Both of them can influence either astringency sensation or bitterness taste.

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Jadoun, Jeries, Ahmad Yazbak, Salwa Rushrush, Amira Rudy, and Hassan Azaizeh. "Identification of a New Antibacterial Sulfur Compound fromRaphanus sativusSeeds." Evidence-Based Complementary and Alternative Medicine 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/9271285.

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Raphanus sativusL. (radish), a member of Brassicaceae, is widely used in traditional medicine in various cultures for treatment of several diseases and disorders associated with microbial infections. The antibacterial activity of the different plant parts has been mainly attributed to several isothiocyanate (ITC) compounds. However, the low correlation between the ITC content and antibacterial activity suggests the involvement of other unknown compounds. The objective of this study was to investigate the antibacterial potential of red radish seeds and identify the active compounds. A crude ethanol seed extract was prepared and its antibacterial activity was tested against five medically important bacteria. The ethanol extract significantly inhibited the growth of all tested strains. However, the inhibitory effect was more pronounced againstStreptococcus pyogenesandEscherichia coli. Bioassay-guided fractionation of the ethanol extract followed by HPLC,1H-NMR,13C-NMR,15N-NMR, and HMBC analysis revealed that the active fraction consisted of a single new compound identified as [5-methylsulfinyl-1-(4-methylsulfinyl-but-3-enyl)-pent-4-enylidene]-sulfamic acid, which consisted of two identical sulfur side chains similar to those found in ITCs. The minimal inhibitory concentration values of the isolated compound were in the range of 0.5–1 mg/mL. These results further highlight the role of radish as a rich source of antibacterial compounds.

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Hakim, Aliefman, Jamaluddin Jamaluddin, I. Nyoman Loka, Saprizal Hadisaputra, and Ayu Rizki Mujiyanti. "Acid-Base Extraction of Anacardic Acid from Cashew Seed Shell." Jurnal Pijar Mipa 16, no. 3 (June 6, 2021): 418. http://dx.doi.org/10.29303/jpm.v16i3.2595.

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Research on the isolation of anacardic acid compounds from cashew nut shells has been carried out. This study aims to develop a method of isolating anacardic acid compounds from cashew nut shells in an easier way but still produces compounds that remain pure. In this study isolation and identification of anacardic acid compounds contained in CNSL was carried out. The results of anacardic acid isolation contained in CNSL in the form of a thick brown extract that has a characteristic dark odor. Anacardic acid was isolated using a maceration method using methanol as a solvent. The results of the isolation of anacardic acid compounds were then tested for purity using a thin layer chromatography test (TLC) using an eluent or a mobile phase of methanol: chloroform. Furthermore anacardic acid compounds were identified using IR spectroscopy and UV-vis spectroscopy. This identification was carried out to prove that the compound obtained was indeed an anacardic acid compound. From the identification results it was found that the compound isolated in this study was indeed an anacardic acid compound. This can be compared with the structure of existing anacardic acid compounds.

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11

Sudirman, Sabri, Nurjanah Nurjanah, and Agoes Mardiono Jacoeb. "Identification of Antioxidant Compounds Structure Large-Leafed Mangrove (Bruguiera gymnorrhiza) Fruit." Jurnal Pengolahan Hasil Perikanan Indonesia 19, no. 2 (August 31, 2016): 94. http://dx.doi.org/10.17844/jphpi.v19i2.13108.

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Antioxidants are compounds that can inhibit or prevent the oxidation of the easily oxidized substrate. One of the plants as a potential source of bioactive compounds and antioxidant activity is large-leafed mangrove (Bruguiera gymnorrhiza). This plant is commonly found in the Pacific region of Southeast Asia, Ryukyu Islands, Micronesia and Polynesia (Samoa) to subtropical regions of Australia and has been used by the society. This study aimed to determine the bioactive compounds structure of large-leafed mangrove has the highest antioxidant activity. The compound structure prediction was done by Nuclear Magnetic Resonance (NMR). The compound structure in the selected antioxidant fractions are flavonol, glikosilfalvon and flavon. Those three compounds are flavonoid compound which has a great role as the one that has antioxidant activity in large-leafed mangrove fruit.

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12

Murini, Tri, Mae Sri Hartati Wahyuningsih, Tri Baskoro Tunggul Satoto, Achmad Fudholi, and Muhammad Hanafi. "ISOLATION AND IDENTIFICATION OF NATURALLY OCCURRING LARVICIDAL COMPOUND ISOLATED FROM ZINGIBER ZERUMBET (L).J.E. SMITH." Asian Journal of Pharmaceutical and Clinical Research 11, no. 2 (February 1, 2018): 189. http://dx.doi.org/10.22159/ajpcr.2018.v11i2.21703.

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Objective: A naturally occurring larvicidal compound is an alternative to eradication of Aedes aegypti larvae. This compound is toxic to larvae but relatively safe for human. Rhizome of Lempuyang gajah (Zingiber zerumbet (L.) J. E. Smith) has been used traditionally to prevent mosquito bites. An initial study indicated that petroleum ether (PE) soluble fraction of the methanol (MeOH) extract of Z. zerumbet was toxic against larvae lethal concentration (LC50), 67.01±2.35 versus 153.57±4.01 ppm (MeOH ext.). Therefore, this study aimed to isolate and identify the compounds with larvicidal activity from Z. zerumbet rhizome.Methods: The PE soluble (PE-soluble) fraction was subjected to a bioassay-guided fractionation and isolation method to obtain four (4) fractions (I-IV). Two compounds (1 and 2) were isolated from Fraction I that was the most active compared to other fractions (II-IV). Compound 1 turned out to be more active than compound 2; therefore, compound 1 was then identified by means of spectroscopic data.Results: Based on the LC50 values, compound 1 was more active than compound 2 (LC50, 41.75±0.05 and LC90, 57.66±3.37 [1] versus 1122.27±1.80 and 1875.69±1.35 ppm [2]), and compound 1 was identified as Zerumbone.Conclusion: Zerumbone was the main active compound; in the future, this compound can be formulated as a standardized preparation based on the content.

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Honma, Masaru, Mark Stubbs, Ian Collins, Paul Workman, Wynne Aherne, and Fiona M. Watt. "Identification of Novel Keratinocyte Differentiation Modulating Compounds by High-Throughput Screening." Journal of Biomolecular Screening 11, no. 8 (December 2006): 977–84. http://dx.doi.org/10.1177/1087057106292556.

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The authors have designed high-throughput screens to identify compounds that promote or inhibit terminal differentiation of primary human epidermal keratinocytes. Eleven known inhibitors of signaling pathways and approximately 4000 compounds of diverse structure were screened using an In-Cell Western system based on immunofluorescent staining of the terminal differentiation marker, involucrin. Staurosporine, a nonspecific protein kinase C inhibitor, and H89, a protein kinase A inhibitor, promoted expression of involucrin. Conversely, U0126, a MEK inhibitor, and SAHA or SBHA, 2 histone deacetylase inhibitors, reduced the expression of involucrin during calcium-induced stratification. In addition, the authors found 1 novel compound that induced keratinocyte differentiation and 2 novel compounds that were inhibitory to calcium-induced differentiation. The differentiation-inducing compound also inhibited growth of a human squamous cell carcinoma line by stimulating both differentiation and apoptosis. Because the compound affected the tumor cells at a lower concentration than primary keratinocytes, it may have potential as an antitumor therapy.

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Wang, ShaoPeng, Yu-Hang Zhang, Jing Lu, Weiren Cui, Jerry Hu, and Yu-Dong Cai. "Analysis and Identification of Aptamer-Compound Interactions with a Maximum Relevance Minimum Redundancy and Nearest Neighbor Algorithm." BioMed Research International 2016 (2016): 1–9. http://dx.doi.org/10.1155/2016/8351204.

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The development of biochemistry and molecular biology has revealed an increasingly important role of compounds in several biological processes. Like the aptamer-protein interaction, aptamer-compound interaction attracts increasing attention. However, it is time-consuming to select proper aptamers against compounds using traditional methods, such as exponential enrichment. Thus, there is an urgent need to design effective computational methods for searching effective aptamers against compounds. This study attempted to extract important features for aptamer-compound interactions using feature selection methods, such as Maximum Relevance Minimum Redundancy, as well as incremental feature selection. Each aptamer-compound pair was represented by properties derived from the aptamer and compound, including frequencies of single nucleotides and dinucleotides for the aptamer, as well as the constitutional, electrostatic, quantum-chemical, and space conformational descriptors of the compounds. As a result, some important features were obtained. To confirm the importance of the obtained features, we further discussed the associations between them and aptamer-compound interactions. Simultaneously, an optimal prediction model based on the nearest neighbor algorithm was built to identify aptamer-compound interactions, which has the potential to be a useful tool for the identification of novel aptamer-compound interactions. The program is available upon the request.

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Bertram, Raymond, and Jukka Hyönä. "The Role of Hyphens at the Constituent Boundary in Compound Word Identification." Experimental Psychology 60, no. 3 (February 1, 2013): 157–63. http://dx.doi.org/10.1027/1618-3169/a000183.

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The current eye-movement study investigated whether a salient segmentation cue like the hyphen facilitates the identification of long and short compound words. The study was conducted in Finnish, where compound words exist in great abundance. The results showed that long hyphenated compounds (musiikki-ilta) are identified faster than concatenated ones (yllätystulos), but short hyphenated compounds (ilta-asu) are identified slower than their concatenated counterparts (kesäsää). This pattern of results is explained by the visual acuity principle ( Bertram & Hyönä, 2003 ): A long compound word does not fully fit in the foveal area, where visual acuity is at its best. Therefore, its identification begins with the access of the initial constituent and this sequential processing is facilitated by the hyphen. However, a short compound word fits in the foveal area, and consequently the hyphen slows down processing by encouraging sequential processing in cases where it is possible to extract and use information of the second constituent as well.

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Mohammed, Abdul Moiz. "UV-Visible Spectrophotometric Method and Validation of Organic Compounds." European Journal of Engineering Research and Science 3, no. 3 (March 13, 2018): 8. http://dx.doi.org/10.24018/ejers.2018.3.3.622.

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Absorption and emission of radiation by a compound at different wavelengths in visible and ultra violet region forms an analytical tool for identification of organic compounds. Researchers and scientists from different fields of chemistry and life sciences are constantly in search of an alternate ways to analyze the chemical reactions involving organic and inorganic compounds. The UV-Visible spectroscopic technique serves as an important and simple technique in finding concentration of molecules in a solution, identification the functional groups identification of conjugated organic compounds. The molar absorption coefficient is an intrinsic property of species, and may be treated as a fingerprint to an organic compound. This papers presents a systematic and detailed validation of organic compounds with the molar absorption coefficient in UV-visible region.

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Ali, Meer Asif, Sugunakar Vuree, Himshikha Goud, Tajamul Hussain, Anuraj Nayarisseri, and Sanjeev Kumar Singh. "Identification of High-affinity Small Molecules Targeting Gamma Secretase for the Treatment of Alzheimer’s Disease." Current Topics in Medicinal Chemistry 19, no. 13 (August 27, 2019): 1173–87. http://dx.doi.org/10.2174/1568026619666190617155326.

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Background: Alzheimers Disease (AD) is a neurodegenerative disease which is characterized by the deposition of amyloid plaques in the brain- a concept supported by most of the researchers worldwide. The main component of the plaques being amyloid-beta (Aβ42) results from the sequential cleavage of Amyloid precursor protein (APP) by beta and gamma secretase. This present study intends to inhibit the formation of amyloid plaques by blocking the action of gamma secretase protein with Inhibitors (GSI). Methods: A number of Gamma Secretase Inhibitors (GSI) were targeted to the protein by molecular docking. The inhibitor having the best affinity was used as a subject for further virtual screening methods to obtain similar compounds. The generated compounds were docked again at the same docking site on the protein to find a compound with higher affinity to inhibit the protein. The highlights of virtually screened compound consisted of Pharmacophore Mapping of the docking site. These steps were followed by comparative assessments for both the compounds, obtained from the two aforesaid docking studies, which included interaction energy descriptors, ADMET profiling and PreADMET evaluations. Results: 111 GSI classified as azepines, sulfonamides and peptide isosteres were used in the study. By molecular docking an amorpholino-amide, compound (22), was identified to be the high affinity compound GSI along with its better interaction profiles.The virtually screened pubchem compound AKOS001083915 (CID:24462213) shows the best affinity with gamma secretase. Collective Pharmacophore mapping (H bonds, electrostatic profile, binding pattern and solvent accesibility) shows a stable interaction. The resulting ADMETand Descriptor values were nearly equivalent. Conclusion: These compounds identified herein hold a potential as Gamma Secretase inhibitors.According to PreADMET values the compound AKOS001083915 is effective and specific to the target protein. Its BOILED-egg plot analysis infers the compound permeable to blood brain barrier.Comparative study for both the compounds resulted in having nearly equivalent properties. These compounds have the capacity to inhibit the protein which is indirectly responsible for the formation of amyloid plaques and can be further put to in vitro pharmacokinetic and dynamic studies.

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Мilyan, P. М., G. V. Kun, Zh І. Milyan, and J. I. Molnar. "Synthesis and Identification of Pb3TeO6 Compound." Фізика і хімія твердого тіла 16, no. 4 (December 15, 2015): 658–60. http://dx.doi.org/10.15330/pcss.16.4.658-660.

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In present work, the physico-chemical analysis of the interaction process for PbO:TeO2=3:1 has been carried out. The ternary compound Pb3TeO6 was obtained by solid-phase reaction; this compound was identified by X-ray diffraction and chemical analysis.

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Miller, Dustin B., and Stephen R. Piccolo. "CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline." F1000Research 9 (October 8, 2020): 1211. http://dx.doi.org/10.12688/f1000research.26848.1.

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A compound heterozygous (CH) variant occurs when a person inherits two alternate alleles, one from each parent, and these alleles occur at different positions within the same gene. Therefore, CH variant identification requires distinguishing maternally from paternally derived nucleotides, a process that requires numerous computational tools. Using such tools can be challenging and often introduce unforeseen challenges such as installation procedures that are operating-system specific, software dependencies, and format requirements for input files. To overcome these challenges, we developed Compound Heterozygous Variant Identification Pipeline (CompoundHetVIP), which uses a single Docker image to encapsulate commonly used software tools for phasing, annotating, and analyzing CH, homozygous alternate, and de novo variants in a series of 13 steps. To begin using our tool, researchers need only install the Docker engine and download the CompoundHetVIP Docker image. The tools provided in CompoundHetVIP can be applied to Illumina whole-genome sequencing data of individual samples or trios (a child and both parents), using VCF or gVCF files as initial input. Each step of the pipeline produces an analysis-ready output file that can be further evaluated. To illustrate its use, we applied CompoundHetVIP to data from a publicly available Ashkenazim trio and identified two genes with candidate CH variants and one gene with a candidate homozygous alternate variant after filtering. While this example uses genomic data from a healthy child, we anticipate that most researchers will use CompoundHetVIP to uncover missing heritability in human diseases and other phenotypes. CompoundHetVIP is open-source software and can be found at https://github.com/dmiller903/CompoundHetVIP; this repository also provides detailed, step-by-step examples.

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Abida, Habib. "Identification of compound channel flow parameters." Journal of Hydrology and Hydromechanics 57, no. 3 (September 1, 2009): 172–81. http://dx.doi.org/10.2478/v10098-009-0016-y.

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Identification of compound channel flow parametersOptimization methods are used to estimate parameters required for routing floods through open compound channels. Besides initial and boundary flow conditions, data required especially include, cross-sectional area (A) of flow and conveyance (K) as functions of flow depth (y) for a representative cross-section of the study reach. Thus, instead of optimizing upon channel's geometric and hydraulic parameters, optimization is performed upon non-physical parameters in assumedA(y) andK(y) relationships. The optimization method selected for this application is the Nelder and Mead Simplex Algorithm. The objective function is expressed in terms of the relative differences between observed and simulated stages and discharges, which are evaluated based on the complete numerical solution of St Venant equations. This approach to formulating the optimization problem was applied to unsteady flow data sets for an experimental reach of the River Main in Northern Ireland. Based on statistical analysis, simulated and observed stages were found to be in good agreement.

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Gerlich, Michael, and Steffen Neumann. "MetFusion: integration of compound identification strategies." Journal of Mass Spectrometry 48, no. 3 (February 27, 2013): 291–98. http://dx.doi.org/10.1002/jms.3123.

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Salemink, P. J. M. "Haemoglobin crystallisation: Identification of the compound." Comparative Haematology International 4, no. 4 (1994): 242–43. http://dx.doi.org/10.1007/bf00185182.

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Miller, Dustin B., and Stephen R. Piccolo. "CompoundHetVIP: Compound Heterozygous Variant Identification Pipeline." F1000Research 9 (February 10, 2021): 1211. http://dx.doi.org/10.12688/f1000research.26848.2.

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Compound Heterozygous (CH) variant identification requires distinguishing maternally from paternally derived nucleotides, a process that requires numerous computational tools. Using such tools often introduces unforeseen challenges such as installation procedures that are operating-system specific, software dependencies that must be installed, and formatting requirements for input files. To overcome these challenges, we developed Compound Heterozygous Variant Identification Pipeline (CompoundHetVIP), which uses a single Docker image to encapsulate commonly used software tools for file aggregation (BCFtools or GATK4), VCF liftover (Picard Tools), joint-genotyping (GATK4), file conversion (Plink2), phasing (SHAPEIT2, Beagle, and/or Eagle2), variant normalization (vt tools), annotation (SnpEff), relational database generation (GEMINI), and identification of CH, homozygous alternate, and de novo variants in a series of 13 steps. To begin using our tool, researchers need only install the Docker engine and download the CompoundHetVIP Docker image. The tools provided in CompoundHetVIP, subject to the limitations of the underlying software, can be applied to whole-genome, whole-exome, or targeted exome sequencing data of individual samples or trios (a child and both parents), using VCF or gVCF files as initial input. Each step of the pipeline produces an analysis-ready output file that can be further evaluated. To illustrate its use, we applied CompoundHetVIP to data from a publicly available Ashkenazim trio and identified two genes with a candidate CH variant and two genes with a candidate homozygous alternate variant after filtering based on user-set thresholds for global minor allele frequency, Combined Annotation Dependent Depletion, and Gene Damage Index. While this example uses genomic data from a healthy child, we anticipate that most researchers will use CompoundHetVIP to uncover missing heritability in human diseases and other phenotypes. CompoundHetVIP is open-source software and can be found at https://github.com/dmiller903/CompoundHetVIP; this repository also provides detailed, step-by-step examples.

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Manzo, Lawaly Maman, Yijuan Cheng, Ling Yang, Jiping Liu, Ya Hui Deng, Li Ping Sun, and Yu Liu. "Small-scale screening program for the identification of cytotoxic Oxazolo[5,4-d]pyrimidine derivatives based on Whole Cell Viability Assay." Indian Journal of Pharmaceutical and Biological Research 3, no. 02 (June 30, 2015): 58–65. http://dx.doi.org/10.30750/ijpbr.3.2.6.

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For over last couple of decades, there has been a robust activity aimed towards the discovery of novel anti-cancer therapeutics. An approach to identify starting points for new drug candidates is high throughput screening of compound library collection. In this work, we describe the application of a Tetrazolium-based, 96-well small scale screening assay to screen a mini library of 19 compounds bearing Oxazolo[5,4-d]pyrimidine structures against human umbilical vein endothelial cells. Primary actives identified against HUVEC were retested and the IC50 value compounds were estimated for HUVEC. The screening program (Primary screening) identified 4 compounds with inhibition rate percentage ≥ 70% each. Retest screening of these compounds, taking into account criteria required for high cytotoxic compounds, afforded a panel of 1 compound for further biological analysis. This compound had IC50 value of 12.19µM, 12.16µM, 10.24µM, 20.43µM for HUVECs, SGC7901, MCF7, and HeLa respectively. Furthermore, a clonogenic assay was performed in order to confirm the cytotoxic activity of the selected compound on the survival and proliferation of MCF7. This compound was found to significantly effect the survival and proliferation of MCF7. Taken together, the selected compound, namely SCYJ32, was found to be highly cytotoxic against the numerous cell lines. Further studies are ongoing in order to unravel various mechanisms of action of this novel small compound.

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Huynh, Q. Khai, Sarah J. Wise, Keith A. Koch, Laurie A. Castonguay, Brian G. Reid, Erinn E. Pagratis, David Koditek, et al. "Screening and Identification of a Novel Class of TGF-β Type 1 Receptor Kinase Inhibitor." Journal of Biomolecular Screening 16, no. 7 (April 26, 2011): 724–33. http://dx.doi.org/10.1177/1087057111405846.

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Transforming growth factor β (TGF-β) type I receptor (activin receptor–like kinase 5, ALK5) has been identified as a promising target for fibrotic diseases. To find a novel inhibitor of ALK5, the authors performed a high-throughput screen of a library of 420 000 compounds using dephosphorylated ALK5. From primary hits of 1521 compounds, 555 compounds were confirmed. In total, 124 compounds were then selected for follow-up based on their unique structures and other properties. Repeated concentration–response testing and final interference assays of the above compounds resulted in the discovery of a structurally novel ALK5 inhibitor (compound 8) (N-(thiophen 2-ylmethyl)-3-(3,4,5 trimethoxyphenyl)imidazo[1,2β]pyridazin 6-amine) with a low IC50 value of 0.7 µM. Compound 8 also inhibited the TGF-β-induced nuclear translocation of SMAD with an EC50 value of 0.8 µM. Kinetic analysis revealed that compound 8 inhibited ALK5 via mixed-type inhibition, suggesting that it may bind to ALK5 differently than other published adenosine triphosphate site inhibitors.

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Saenz, Jose B., Teresa A. Doggett, and David B. Haslam. "Identification and Characterization of Small Molecules That Inhibit Intracellular Toxin Transport." Infection and Immunity 75, no. 9 (June 18, 2007): 4552–61. http://dx.doi.org/10.1128/iai.00442-07.

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ABSTRACT Shiga toxin (Stx), cholera toxin (Ctx), and the plant toxin ricin are among several toxins that reach their intracellular destinations via a complex route. Following endocytosis, these toxins travel in a retrograde direction through the endosomal system to the trans-Golgi network, Golgi apparatus, and endoplasmic reticulum (ER). There the toxins are transported across the ER membrane to the cytosol, where they carry out their toxic effects. Transport via the ER from the cell surface to the cytosol is apparently unique to pathogenic toxins, raising the possibility that various stages in the transport pathway can be therapeutically targeted. We have applied a luciferase-based high-throughput screen to a chemical library of small-molecule compounds in order to identify inhibitors of Stx. We report two novel compounds that protect against Stx and ricin inhibition of protein synthesis, and we demonstrate that these compounds reversibly inhibit bacterial transport at various stages in the endocytic pathway. One compound (compound 75) inhibited transport at an early stage of Stx and Ctx transport and also provided protection against diphtheria toxin, which enters the cytosol from early endosomes. In contrast, compound 134 inhibited transport from recycling endosomes through the Golgi apparatus and protected only against toxins that access the ER. Small-molecule compounds such as these will provide insight into the mechanism of toxin transport and lead to the identification of compounds with therapeutic potential against toxins routed through the ER.

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Kunig, Verena, Marco Potowski, Anne Gohla, and Andreas Brunschweiger. "DNA-encoded libraries – an efficient small molecule discovery technology for the biomedical sciences." Biological Chemistry 399, no. 7 (June 27, 2018): 691–710. http://dx.doi.org/10.1515/hsz-2018-0119.

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Abstract DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.

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Nalla, Viswanadh, Aslam Shaikh, Sanket Bapat, Renu Vyas, M. Karthikeyan, P. Yogeeswari, D. Sriram, and M. Muthukrishnan. "Identification of potent chromone embedded [1,2,3]-triazoles as novel anti-tubercular agents." Royal Society Open Science 5, no. 4 (April 2018): 171750. http://dx.doi.org/10.1098/rsos.171750.

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A series of 20 novel chromone embedded [1,2,3]-triazoles derivatives were synthesized via an easy and convenient synthetic procedure starting from 2-hydroxy acetophenone. The in vitro anti-mycobacterial evaluation studies carried out in this work reveal that seven compounds exhibit significant inhibition against Mycobacterium tuberculosis H37Rv strain with MIC in the range of 1.56–12.5 µg ml −1 . Noticeably, compound 6s was the most potent compound in vitro with a MIC value of 1.56 µg ml −1 . Molecular docking and chemoinformatics studies revealed that compound 6s displayed drug-like properties against the enoyl-acyl carrier protein reductase of M. tuberculosis further establishing its potential as a potent inhibitor.

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Song, Xuelei S., Jiaping Zhang, Xun Chen, Oksana Palyha, Christine Chung, Lisa M. Sonatore, Larissa Wilsie, et al. "Identification of DGAT2 Inhibitors Using Mass Spectrometry." Journal of Biomolecular Screening 21, no. 2 (September 24, 2015): 117–26. http://dx.doi.org/10.1177/1087057115607463.

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Mass spectrometry offers significant advantages over other detection technologies in the areas of hit finding, hit validation, and medicinal chemistry compound optimization. The foremost obvious advantage is the ability to directly measure enzymatic product formation. In addition, the inherent sensitivity of the liquid chromatography/mass spectrometry (LC/MS) approach allows the execution of enzymatic assays at substrate concentrations typically at or below substrate Km. Another advantage of the LC/MS approach is the ability to assay impure enzyme systems that would otherwise be difficult to prosecute with traditional labeled methods. This approach was used to identify inhibitors of diacylglycerol O-acyltransferase-2 (DGAT2), a transmembrane enzyme involved in the triglyceride (TG) production pathway. The LC/MS approach was employed because of its increased assay window (compared with control membranes) of more than sevenfold compared with less than twofold with a conventional fluorogenic assay. The ability to generate thousands of dose-dependent IC50 data was made possible by the use of a staggered parallel LC/MS system with fast elution gradients. From the hit-deconvolution efforts, several structural scaffold series were identified that inhibit DGAT2 activity. Additional profiling of one chemotype in particular identified two promising reversible and selective compounds (compound 15 and compound 16) that effectively inhibit TG production in mouse primary hepatocytes.

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Anderson, Steven N., Danli L. Towne, David J. Burns, and Usha Warrior. "A High-Throughput Soft Agar Assay for Identification of Anticancer Compound." Journal of Biomolecular Screening 12, no. 7 (October 2007): 938–45. http://dx.doi.org/10.1177/1087057107306130.

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A 384-well soft agar assay was developed to identify potential novel anticancer compounds. Normally used to detect cell transformation, the assay is used here to quantitate cell proliferation in a 3-dimensional (3-D) anchorage-independent format. HCC827 cells, which are highly sensitive to epithelial growth factor receptor (EGFR) tyrosine kinase inhibitors, were used to develop the method and a set of 9600 compounds used to validate the assay. Results were compared to a monolayer assay using the same compound set. The assay provides a robust method to discover compounds that could be missed using traditional monolayer formats. ( Journal of Biomolecular Screening 2007:938-945)

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Moriev, R., O. Vasylchenko, M. Platonov, O. Grygorenko, K. Volkova, and S. Zozulya. "Identification of Novel IGF1R Kinase Inhibitors by Molecular Modeling and High-Throughput Screening." Acta Naturae 5, no. 2 (June 15, 2013): 90–99. http://dx.doi.org/10.32607/20758251-2013-5-2-90-99.

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The aim of this study was to identify small molecule compounds that inhibit the kinase activity of the IGF1 receptor and represent novel chemical scaffolds, which can be potentially exploited to develop drug candidates that are superior to the existing experimental anti-IGF1R therapeuticals. To this end, targeted compound libraries were produced by virtual screening using molecular modeling and docking strategies, as well as the ligand-based pharmacophore model. High-throughput screening of the resulting compound sets in a biochemical kinase inhibition assay allowed us to identify several novel chemotypes that represent attractive starting points for the development of advanced IGF1R inhibitory compounds.

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Matson, Sandra L., Moneesh Chatterjee, David A. Stock, John E. Leet, Elizabeth A. Dumas, Christian D. Ferrante, William E. Monahan, et al. "Best Practices in Compound Management for Preserving Compound Integrity and Accurately Providing Samples for Assays." Journal of Biomolecular Screening 14, no. 5 (May 29, 2009): 476–84. http://dx.doi.org/10.1177/1087057109336593.

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Preserving the integrity of the compound collection and providing high-quality materials for drug discovery in an efficient and cost-effective manner are 2 major challenges faced by compound management (CM) at Bristol-Myers Squibb (BMS). The demands on CM include delivering hundreds of thousands of compounds a year to a variety of operations. These operations range from single-compound requests to hit identification support and just-in-time assay plate provision for lead optimization. Support needs for these processes consist of the ability to rapidly provide compounds as solids or solutions in a variety of formats, establishing proper long- and short-term storage conditions and creating appropriate methods for handling concentrated, potent compounds for delivery to sensitive biological assays. A series of experiments evaluating the effects of processing compounds with volatile solvents, storage conditions that can induce freeze/thaw cycles, and the delivery of compounds were performed. This article presents the results of these experiments and how they affect compound integrity and the accuracy of compound management processes. ( Journal of Biomolecular Screening 2009:476-484)

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Asmawati, Asmawati. "Identification of inorganic compounds in eggshell as a dental remineralization material." Journal of Dentomaxillofacial Science 2, no. 3 (December 1, 2017): 168. http://dx.doi.org/10.15562/jdmfs.v2i3.622.

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Objective: Many patients suffer from sensitive teeth after bleaching that can cause demineralization of enamel and widening of dentinal tubules. Hence, researchers are looking for natural ingredients for enamel remineralization material include chicken egg shells because it contain calcium carbonate that can restore lost inorganic compounds. This study aimed to identify inorganic compound in eggshell as dental remineralization agent.Materials and methods:This study was an experimental laboratory with with post test only control group design. The research sample was five maxillary central incisor that has been applied with 35% hydrogen peroxide bleaching material in different time range 1 hour, 1 hour 30 minutes, 2 hours, 2 hours 30 minutes and 3 hours. Then, samples were applied with chicken egg shells gel for 14 consecutive days. Identification of inorganic compound was analyzed using Energy Dispersive X-ray Spectroscopy (EDS).Results: The application of chicken egg shells gel do not cause a significant difference in the composition of enamel compound between control group and treatment group.Conclusions: There is an increasing number of inorganic compounds in samples that had been applied with eggshell gel such as calcium, phosphorus, magnesium, chlorine, oxygen, and aluminium.

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Violet, Violet. "IDENTIFIKASI PEMANFAATAN TRADISIONAL DAN PENAPISAN SENYAWA FITOKIMIA EKTRAK DAUN BINTANGUR (Callophyllum soulatri Burm F.)." EnviroScienteae 14, no. 1 (April 28, 2018): 70. http://dx.doi.org/10.20527/es.v14i1.4896.

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Bintangur (Callophylum soulatri) is one type of Family Callophylleae which is widely found in the forests of Borneo. This research attempts to identify the traditional using of Bintangur plant as a medicinal material and get the result of phytochemical compound from Bintangur leaf extract. Identification of the use of Bintangur plants is done using semi-structured interview techniques and literature review. The phytochemical compound preliminary test is carried out qualitatively by color change detection. Bintangur leaves can eliminate the disease vertigo (dizziness) and migraine. The dominant phytochemical compounds are flavonoids, steroid, and tannin. Phytochemical compounds that also dominant are phenol hydrocarbons and saponins. The alkaloid compound is not present in Bintangur leaves. The identification of phytochemical compounds from Bintangur leaf identifies the potential utilization of phytochemical compounds for various medicinal goals. The detection of steroid compounds with high concentrations indicates that Bintangur leaf has the potential to be used as a medicinal material to relieve chronic fatigue and pain. The presence of phenol compounds such as flavonoids, phenol hydrocarbons, and tannins indicates that the Bintangur leaf has bioactivity as antioxidants, antibacterials and anticancer.

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Bano, Saddia, Muhammad Asif Rasheed, Farrukh Jamil, Muhammad Ibrahim, and Sumaira Kanwal. "In Silico Identification of Novel Apolipoprotein E4 Inhibitor for Alzheimer’s Disease Therapy." Current Computer-Aided Drug Design 15, no. 1 (December 14, 2018): 97–103. http://dx.doi.org/10.2174/1573409914666181008164209.

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Introduction: Apolipoprotein E4 (ApoE) is a major genetic factor for developing Alzheimer’s disease (AD). It plays a vital role in brain to maintain a constant supply of neuronal lipids for rapid and dynamic membrane synthesis. Aggregation of beta amyloid plaques (Aβ) and neurofibrillary tangles in brain are responsible for onset of AD. The current study is designed to predict a drug against over activity of apoE4. 22 natural compounds (marine, microorganism and plant derivative) were used in current study. Methods: These compounds were used as inhibitors to target apoE4 protein activity. Moreover, six synthetic compounds were docked with target protein to compare and analyze the docking results with natural compounds. S-Allyl-L-Cysteine, Epicatechin Gallate and Fulvic acid showed highest binding affinity (-7.1, - 7 and -7 kcal /mol respectively). Analysis of the docked complex showed that Epicatechin Gallate bonded with Gln156 and Asp35. Furthermore, Fulvic Acid showed hydrogen bonding with Glu27. Among synthetic compound, Tideglusib had highest binding affinity with target protein but did not show hydrogen bonding with any amino acid residue. Moreover, a natural compound S-Allyl-LCysteine also showed highest binding affinity but did not show hydrogen bonding with any amino acid residue. Results and Conclusion: Our study highlighted Epicatechin Gallate as a potential lead compound on the basis of binding affinity and hydrogen bonding to inhibit the progression of AD.

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Paal, Michael, Katharina Habler, and Michael Vogeser. "Mass spectrometric sample identification with indicator compounds introduced via labeled sample tubes." Clinical Chemistry and Laboratory Medicine (CCLM) 59, no. 1 (January 26, 2021): 147–54. http://dx.doi.org/10.1515/cclm-2020-0667.

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AbstractObjectivesThe risk of sample confusion continues to be a challenge for the pre-analytical part of the overall testing process. We here describe a novel system to track samples based on a chemical code labeling of test tubes with unique combinations of indicator compounds, which are naturally not present in specimens of human origin. As part of the sample vessel filling, the liquid specimens are permanently labeled with the compound code that can be tracked back to the primary tube.MethodsAs a proof of concept we used 10 stable-isotope-labeled derivates of medical drugs as indicator substances to create a combinatory 10-digit binary number ID for individual test tubes, i.e. presence/absence of the respective compound. For this purpose, combinations of indicator compounds were provided in evaporated form in polypropylene tubes prior to filling with anonymized patient whole blood and corresponding plasmas subjected to liquid chromatography tandem-mass spectrometry designed to detect the 10 indicator compounds.ResultsIn the blind analysis, we correctly identified 307 different whole blood samples by readout of a 10-digit binary number ID based on the detection of indicator compounds with respect to their presence and number.ConclusionsWe have demonstrated the feasibility of an internal labeling procedure for diagnostic samples with mass spectrometry-based readout of dissolved indicator compound combinations as a binary number ID. With an increasing number of coding compounds (≫10) a vast number of combinations for sample labeling can be realized beyond the proof of concept setting studied herein.

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Sawyer, Tomi K. "New screening tools for lead compound identification." Nature Chemical Biology 1, no. 3 (August 2005): 125. http://dx.doi.org/10.1038/nchembio0805-125.

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Lopez Chau, Asdrubal, Rafael Rojas Hernandez, Valentin Trujillo Mora, Jair Cervantes Canales, Lisbeth Rodriguez Mazahua, and Farid Garcia Lamont. "Detection of Compound Leaves for Plant Identification." IEEE Latin America Transactions 15, no. 11 (November 2017): 2185–90. http://dx.doi.org/10.1109/tla.2017.8070425.

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Fan, Xiaofeng, M. M. Li, David J. Singh, Qing Jiang, and W. T. Zheng. "Identification of a potential superhard compound ReCN." Journal of Alloys and Compounds 631 (May 2015): 321–27. http://dx.doi.org/10.1016/j.jallcom.2015.01.119.

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Ma, Jingjing, Emma Wu, Ye Li, William Seibel, Le Shen, Fatemeh Khalili, and Christopher Weber. "IDENTIFICATION OF SELETIVE CLAUDIN CATION CHANNEL BLOCKERS." Inflammatory Bowel Diseases 27, Supplement_1 (January 1, 2021): S25—S26. http://dx.doi.org/10.1093/ibd/izaa347.057.

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Abstract Compromised epithelial barrier function is known to be associated with inflammatory bowel disease (IBD) and may contribute to disease development. One mechanism of barrier dysfunction is increased expression of paracellular tight junction ion and water channels formed by claudins. Claudin-2 and -15 are two such channels. We hypothesize that blocking these channels could be a viable therapeutic approach to treat diarrhea. In an effort to develop blockers of these channels, we turn to our previously developed and validated in silico models of claudin-15 (Samanta et al. 2018). We reasoned that compounds that can bind with the interior of claudin pores can limit paracellular water and ion flux. Thus, we used docking algorithms to search for putative small molecules that bind in the claudin-15 pore. AutoDock Vina was initially used to assess rigid docking using small compound databases. The small molecules were analyzed based on binding affinity to the pore and visualized using VMD for their potential blockage of the channel. Clusters of binding modes were identified based on the prominent interacting residues of the protein with the small molecules. We initially screened 10,500 compounds from within the UIC Centre for Drug Discovery and a cross-section of 10,000 compounds from the NCI open compound repository. This initial screen allowed us to identify 2 first-in-class selective claudin-15 blockers with efficacy in MDCK monolayers induced to express claudin-15 and in wildtype duodenum. Next, we screened the entire NCI open compound repository for additional molecules structurally related to our best initially identified molecule and this has allowed us to identify 13 additional molecules that increase TER of claudin-15 expressing MDCK monolayers by 90–160%. Additionally, these molecules possess similar structural components that will be collected in a fragment library and explored through molecular dynamics simulations. We also developed a claudin-2 homology model on which we are performing docking studies and in vitro measurements, which we expect will result in similar candidate ligands for blocking claudin-2. Our study will provide important insight into the role of claudin-dependent cation permeability in fundamental physiology, which we believe will lead to the utility of claudin blockers as a novel and much needed approach to treat diseases such as IBD.

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Palmer, Stephanie O., Yanmei Hu, Megan Keniry, and James M. Bullard. "Identification of Chemical Compounds That Inhibit Protein Synthesis in Pseudomonas aeruginosa." SLAS DISCOVERY: Advancing the Science of Drug Discovery 22, no. 6 (November 21, 2016): 775–82. http://dx.doi.org/10.1177/1087057116679591.

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Four inhibitory compounds were identified using a poly-uridylic acid (polyU) mRNA-directed aminoacylation/translation (A/T) protein synthesis system composed of phenylalanyl-tRNA synthetases (PheRS), ribosomes, and ribosomal factors from Pseudomonas aeruginosa in an in vitro screen of a synthetic compound library. The compounds were specific for inhibition of bacterial protein synthesis. In enzymatic assays, the compounds inhibited protein synthesis with IC50 values ranging from 20 to 60 μM. Minimum inhibitory concentrations (MICs) were determined in cultures for a panel of pathogenic organisms, including Enterococcus faecalis, Escherichia coli, Haemophilus influenzae, P. aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae. All the compounds were observed to have broad-spectrum activity and inhibited an efflux pump mutant strain of P. aeruginosa with MICs of 0.5–16 μg/mL. The molecular target of two compounds was determined to be PheRS. These two compounds were bacteriostatic against both Gram-positive and Gram-negative pathogens. In competition assays, they were not observed to compete with the natural substrates ATP or phenylalanine for active site binding. The other two compounds directly inhibited the ribosome and were bactericidal against both Gram-positive and Gram-negative pathogens. In cytotoxicity MTT testing in human cell lines, the compounds were shown to be from 2500- to 30,000-fold less active than the control staurosporine.

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Li, Hong, Jung Park, Xiang Su, Kyung Kim, Jong Kang, Young Kim, Young Kim, and Seo Yang. "Identification of Anti-Melanogenesis Constituents from Morus alba L. Leaves." Molecules 23, no. 10 (October 8, 2018): 2559. http://dx.doi.org/10.3390/molecules23102559.

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The individual parts of Morus alba L. including root bark, branches, leaves, and fruits are used as a cosmetic ingredient in many Asian countries. This study identified several anti-melanogenesis constituents in a 70% ethanol extract of M. alba leaves. The ethyl acetate fraction of the initial ethanol extract decreased the activity of tyrosinase, a key enzyme in the synthetic pathway of melanin. Twelve compounds were isolated from this fraction and their structures were identified based on spectroscopic spectra. Then, the authors investigated the anti-melanogenesis effects of the isolated compounds in B16-F10 mouse melanoma cells. Compounds 3 and 8 significantly inhibited not only melanin production but also intracellular tyrosinase activity in alpha-melanocyte-stimulating-hormone (α-MSH)-induced B16-F10 cells in a dose-dependent manner. These same compounds also inhibited melanogenesis-related protein expression such as microphthalmia-associated transcription factor (MITF), tyrosinase, and tyrosinase-related protein-1 (TRP-1). Compound 3 modulated the cAMP-responsive element-binding protein (CREB) and p38 signaling pathways in α-MSH-activated B16-F10 melanoma cells, which resulted in the anti-melanogenesis effects. These results suggest that compound 3, isolated from M. alba leaves, could be used to inhibit melanin production via the regulation of melanogenesis-related protein expression.

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Fauzia, Ditya Vega, Dewi Kusrini, and Enny Fachriyah. "Isolation and Testing of Bacteria from Steroid Compounds obtained from Anting-anting Leaf (Acalypha indica L.)." Jurnal Kimia Sains dan Aplikasi 21, no. 2 (April 30, 2018): 64–69. http://dx.doi.org/10.14710/jksa.21.2.64-69.

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Isolation of steroid compounds from the leaves of the earrings (Acalypha indica L.) and the antibacterial test has been performed. This study aims to obtain information about secondary metabolite compound leaves of Anting-anting, obtaining and identifying steroid isolates from the leaves of Anting-anting and knowing the antibacterial activity of the positive fraction of steroid compounds. The research stages include sample preparation, phytochemical test, isolation, separation, purification of steroid compounds, identification of steroid isolates using LC-MS/MS, and antibacterial test by paper disc method. The results of phytochemical screening show that the leaves of the earrings contain alkaloid compounds, flavonoids, steroids, saponins, tannins, and quinones. From the results of steroid isolation, we found steroid isolates weighing 0.0065 grams (0.0058%). Identification of steroid isolates using LC-MS/MS at a retention time of 7.49 min with [M+H]+ 399 m/z indicated the presence of a brassicasterol compound. The results of antibacterial test of fraction A from chloroform extract containing steroid compound showed antibacterial activity against Staphylococcus aureus bacteria and Escherichia coli bacteria.

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Pink, Mario, Nisha Verma, Christian Kersch, and Simone Schmitz-Spanke. "Identification and characterization of small organic compounds within the corona formed around engineered nanoparticles." Environmental Science: Nano 5, no. 6 (2018): 1420–27. http://dx.doi.org/10.1039/c8en00161h.

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The biological identity of nanoparticles depends on the organic compounds bound to the surface; however, compounds other than proteins are largely uninvestigated. This study highlights the presence of unique compound profiles within the corona of the tested nanoparticles.

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da Silva, Luciane S., Uessiley R. Barbosa, Lívia do C. Silva, Célia MA Soares, Maristela Pereira, and Roosevelt A. da Silva. "Identification of a new antifungal compound against isocitrate lyase of Paracoccidioides brasiliensis." Future Microbiology 14, no. 18 (December 2019): 1589–606. http://dx.doi.org/10.2217/fmb-2019-0166.

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Aim: To perform virtual screening of compounds based on natural products targeting isocitrate lyase of Paracoccidioides brasiliensis. Materials & methods: Homology modeling and molecular dynamics simulations were applied in order to obtain conformational models for virtual screening. The selected hits were tested in vitro against enzymatic activity of ICL of the dimorphic fungus P. brasiliensis and growth of the Paracoccidioides spp. The cytotoxicity and selectivity index of the compounds were defined. Results & conclusion: Carboxamide, lactone and β-carboline moieties were identified as interesting chemical groups for the design of new antifungal compounds. The compounds inhibited ICL of the dimorphic fungus P. brasiliensis activity. The compound 4559339 presented minimum inhibitory concentration of 7.3 μg/ml in P. brasiliensis with fungicidal effect at this concentration. Thus, a new potential antifungal against P. brasiliensis is proposed.

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Quilliam, Michael A., Brian E. McCarry, Ken H. Hoo, Dennis R. McCalla, and Susan Vaitekunas. "Identification of the photolysis products of nitrofurazone irradiated with laboratory illumination." Canadian Journal of Chemistry 65, no. 5 (May 1, 1987): 1128–32. http://dx.doi.org/10.1139/v87-188.

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Illumination of aqueous or organic solutions of nitrofurazone, 1, with fluorescent or tungsten light caused the appearance of two new compounds, 2 and 3. Compound 2, which eluted just before nitrofurazone on a reverse phase hplc column, had a mass spectrum identical to that of 1 and converted back to 1 at a rate proportional to the temperature and the polarity of the solvent when allowed to sit in the dark. High resolution proton nmr spectroscopy provided conclusive evidence that compound 2 is the syn isomer of 1. Compound 3 had a retention time, ultraviolet spectrum, and mass spectrum that were indistinguishable from those of synthetic 5-nitrofuraldehyde azine. The toxicity of 3 to E. coli was determined to be the same as 1 while its mutagenicity was over 10-fold lower. No detectable cross-links were formed in the DNA of E. coli in the presence of compound 3. Thus, it is unlikely that the relatively small amounts of the azine 3 formed have much influence on the antibacterial potency or mutagenicity of nitrofurazone solutions. However, these results do confirm the desirability of conducting experiments with these agents in the dark or under yellow light. Photochemical formation of syn isomers was also observed with two other Schiff 's base nitrofuran derivatives, nitrofurantoin and furazolidone.

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Shrivastava, Rashmi, and Jyotsana Mishra. "Extraction, Phytochemical Screening, Isolation and Identification of Bioactive Compounds from Extract of the plant Euphorbia Thymifolia Linn." Journal of Drug Delivery and Therapeutics 9, no. 3 (May 15, 2019): 107–13. http://dx.doi.org/10.22270/jddt.v9i3.2608.

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Medicinal plants play an important role in the development of potent therapeutic agents. Plant based drugs provide outstanding contribution to modern therapeutics as a source of many valuable secondary metabolites which serves as plant defense mechanisms against predator such as microorganism, insects and herbivores which have been proved to be potentially active compounds. Euphorbia Thymifolia Linn (E. Thymifolia) is commonly known as ‘duddi’ or in Sanskrit means Laghu didhika or Raktavindaka. It belongs to the family Euphorbiceae. This plant is bitter, acrid, sweet and used as thermogenic, laxative and diuretic. This plant is widely used in the ayurveda to cure many diseases like vitiated condition of constipation, helminthiasis and ringworm skin diseases and leprosy. The aim of the present study is to examine E.Thymifolia Linn whole plant for phytochemical profile, Isolation and Identification of bioactive compounds. Qualitative analysis of various phytochemical constituents was determined by the well-known test protocol available in the literature. Isolation and characterization of bioactive compound from methanolic extract of E. Thymifolia has been conducted. The bioactive compound from methanolic extracts was isolated by several processes, such as TLC, column chromatography and preparative TLC. The isolated bioactive compound is identified by UV-Vis spectrophotometer, FT-IR, 1H, 13C-NMR and Mass. The obtained compound is continued to the preparative TLC using chloroform: methanol (50:50, v/v) as eluent. The UV-Vis spectrum showed one peaks of maximum absorbance at 312.8nm. Then, the FT-IR spectrum showed several peaks that confirmed the presence of functional group of derivative of compound, i.e. 669.05, 928.58, 1070.85, 1215.51 and 1710.07cm-1. 1H and 13C-NMR spectrum confirmed the bioactive compound present in plant. Phytochemical analysis revealed the presence of alkaloids, glycosides, phenols, flavonoids, tannins. The findings of the present study will be helpful to phytochemists, pharmacologists and pharmaceutical industries. Keywords: Euphorbia Thymifolia, Qualitative phytochemical, Isolation, Bioactive compounds

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Wang, Xinping, Yuhui Zhao, Peiyan Sun, Min Ji, and Mutai Bao. "Automatic integration method for single and multiple peaks in the GC and GC-MS chromatograms of characteristic oil compounds." Analytical Methods 7, no. 6 (2015): 2670–79. http://dx.doi.org/10.1039/c4ay03088e.

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In oil fingerprinting studies, hundreds of compound peaks (including saturated and aromatic hydrocarbons) need to be integrated for the identification and quantification of characteristic oil compounds.

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Cui, Qinghua, Han Cheng, Rui Xiong, Gang Zhang, Ruikun Du, Manu Anantpadma, Robert Davey, and Lijun Rong. "Identification of Diaryl-Quinoline Compounds as Entry Inhibitors of Ebola Virus." Viruses 10, no. 12 (November 30, 2018): 678. http://dx.doi.org/10.3390/v10120678.

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Ebola virus is the causative agent of Ebola virus disease in humans. The lethality of Ebola virus infection is about 50%, supporting the urgent need to develop anti-Ebola drugs. Glycoprotein (GP) is the only surface protein of the Ebola virus, which is functionally critical for the virus to attach and enter the host cells, and is a promising target for anti-Ebola virus drug development. In this study, using the recombinant HIV-1/Ebola pseudovirus platform we previously established, we evaluated a small molecule library containing various quinoline compounds for anti-Ebola virus entry inhibitors. Some of the quinoline compounds specifically inhibited the entry of the Ebola virus. Among them, compound SYL1712 was the most potent Ebola virus entry inhibitor with an IC50 of ~1 μM. The binding of SYL1712 to the vial glycoprotein was computationally modeled and was predicted to interact with specific residues of GP. We used the time of the addition assay to show that compound SYL1712 blocks Ebola GP-mediated entry. Finally, consistent with being an Ebola virus entry inhibitor, compound SYL1712 inhibited infectious Ebola virus replication in tissue culture under biosafety level 4 containment, with an IC50 of 2 μM. In conclusion, we identified several related molecules with a diaryl-quinoline scaffold as potential anti-EBOV entry inhibitors, which can be further optimized for anti-Ebola drug development.

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Drieghe, Denis, Lei Cui, Guoli Yan, Xuejun Bai, Hui Chi, and Simon P. Liversedge. "The morphosyntactic structure of compound words influences parafoveal processing in Chinese reading." Quarterly Journal of Experimental Psychology 71, no. 1 (January 2018): 190–97. http://dx.doi.org/10.1080/17470218.2017.1307426.

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In an eye movement experiment employing the boundary paradigm, we compared parafoveal preview benefit during the reading of Chinese sentences. The target word was a two-character compound that had either a noun–noun or an adjective–noun structure each sharing an identical noun as the second character. The boundary was located between the two characters of the compound word. Prior to the eyes crossing the boundary, the preview of the second character was presented either normally or was replaced by a pseudocharacter. Previously, Juhasz, Inhoff, and Rayner observed that inserting a space into a normally unspaced compound in English significantly disrupted processing and that this disruption was larger for adjective–noun compounds than for noun–noun compounds. This finding supports the hypothesis that, at least in English, for adjective–noun compounds, the noun is more important for lexical identification than the adjective, while for noun–noun compounds, both constituents are similar in importance for lexical identification. Our results indicate a similar division of the importance of compounds in reading in Chinese as the pseudocharacter preview was more disruptive for the adjective–noun compounds than for the noun–noun compounds. These findings also indicate that parafoveal processing can be influenced by the morphosyntactic structure of the currently fixated character.

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Journal articles on the topic 'Compound identification'

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