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Journal articles on the topic 'Hit identification'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Yi, Xiangyan, Lian Xue, Tim Thomas, and Jonathan B. Baell. "Action plan for hit identification (APHID): KAT6A as a case study." Future Medicinal Chemistry 12, no. 5 (March 2020): 423–37. http://dx.doi.org/10.4155/fmc-2019-0212.

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Here, we describe our action plan for hit identification (APHID) that guides the process of hit triage, with elimination of less tractable hits and retention of more tractable hits. We exemplify the process with reference to our high-throughput screening (HTS) campaign against the enzyme, KAT6A, that resulted in successful identification of a tractable hit. We hope that APHID could serve as a useful, concise and digestible guide for those involved in HTS and hit triage, especially those that are relatively new to this exciting and continually evolving technology.

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2

Volynets, Galyna P., Sergiy A. Starosyla, Mariia Yu Rybak, Volodymyr G. Bdzhola, Oksana P. Kovalenko, Vasyl S. Vdovin, Sergiy M. Yarmoluk, and Michail A. Tukalo. "Dual-targeted hit identification using pharmacophore screening." Journal of Computer-Aided Molecular Design 33, no. 11 (November 2019): 955–64. http://dx.doi.org/10.1007/s10822-019-00245-5.

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3

Bergeron, Charles, Michael Krein, Gregory Moore, Curt M. Breneman, and Kristin P. Bennett. "Modeling Choices for Virtual Screening Hit Identification." Molecular Informatics 30, no. 9 (August 17, 2011): 765–77. http://dx.doi.org/10.1002/minf.201100092.

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4

Morley, Andrew D., Angelo Pugliese, Kristian Birchall, Justin Bower, Paul Brennan, Nathan Brown, Tim Chapman, et al. "Fragment-based hit identification: thinking in 3D." Drug Discovery Today 18, no. 23-24 (December 2013): 1221–27. http://dx.doi.org/10.1016/j.drudis.2013.07.011.

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5

Oo, Thein H., and Cristhiam Mauricio Rojas Hernandez. "Diagnostic Performance of Heparin-Platelet Factor 4 Antibodies in the Identification of Heparin-Induced Thrombocytopenia in Cancer Population." Blood 134, Supplement_1 (November 13, 2019): 4896. http://dx.doi.org/10.1182/blood-2019-132072.

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Introduction: Cancer patients appear to have a higher risk of heparin induced thrombocytopenia (HIT) related complications than non-cancer patients; yet data on the performance of conventional diagnostic tools for HIT in cancer is limited. Our aim was to determine among cancer patients with a 4T score ≥ 4, the performance of the conventional cut-off for HIT antibody testing (IgG anti PF4) to discriminate between serotonin release assay (SRA) positive and negative cases. Methods: Retrospective and prospective analysis of cases (2002-2019) was performed of the electronic medical records of adult cancer patients at MD Anderson Cancer Center with suspected HIT. Cases were included in the analysis if the 4T score was ≥ 4 and investigated with IgG anti-PF4 optical density (HIT OD) and SRA. Logistic regression model and the receiver operating characteristic curves were conducted to identify the sensitivity and specificity of different cut-off points for the HIT OD to discriminate HIT cases based on the SRA status. Results: Among 50 cases, 18 were SRA positive. Median HIT OD was 1.03. At a cut-off point of 0.4, the HIT OD performed with a sensitivity of 0.89 and a specificity of 0.50 to discriminate the cases of SRA positive HIT. When the cut-off HIT OD was 1.0, the sensitivity was 0.78 with a specificity of 0.66. Conclusions: Our findings suggest that in cancer patients the performance of IgG anti-PF4 is similar to that of non-cancer patients for the identification of HIT cases. Disclosures Oo: Janssen and Janssen: Other: Research: site co-investigator ; Medical Education Speakers Network: Honoraria.

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6

E. Nichols, Sara, Robert V. Swift, and Rommie E. Amaro. "Rational Prediction with Molecular Dynamics for Hit Identification." Current Topics in Medicinal Chemistry 12, no. 18 (September 1, 2012): 2002–12. http://dx.doi.org/10.2174/156802612804910313.

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7

Nichols, Sara E., Robert V. Swift, and Rommie E. Amaro. "Rational Prediction with Molecular Dynamics for Hit Identification." Current Topics in Medicinal Chemistry 12, no. 18 (January 7, 2013): 2002–12. http://dx.doi.org/10.2174/1568026611212180007.

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Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline.

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8

Protopopov, M. V., S. A. Starosyla, O. V. Borovykov, V. N. Sapelkin, Y. V. Bilokin, V. G. Bdzhola, and S. M. Yarmoluk. "Hit identification of CK2 inhibitors by virtual screening." Biopolymers and Cell 33, no. 4 (August 31, 2017): 291–301. http://dx.doi.org/10.7124/bc.00095b.

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9

Park, Jun-Kyu, Suwoong Lee, Aaron Park, and Sung-June Baek. "Adaptive Hit-Quality Index for Raman Spectrum Identification." Analytical Chemistry 92, no. 15 (June 4, 2020): 10291–99. http://dx.doi.org/10.1021/acs.analchem.0c00209.

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10

Goodnow, Robert A. "Hit and lead identification: Integrated technology-based approaches." Drug Discovery Today: Technologies 3, no. 4 (December 2006): 367–75. http://dx.doi.org/10.1016/j.ddtec.2006.12.009.

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11

Besch, Guillaume, Dejan Ilic, Marc Ginet, Clément d’Audigier, Philippe Nguyen, David Ferreira, Emmanuel Samain, Guillaume Mourey, and Sebastien Pili-Floury. "Identification of Heparin-Induced Thrombocytopenia in Surgical Critically Ill Patients by Using the HIT Expert Probability Score: An Observational Pilot Study." Journal of Clinical Medicine 11, no. 6 (March 10, 2022): 1515. http://dx.doi.org/10.3390/jcm11061515.

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Background: Heparin-induced thrombocytopenia (HIT) remains a challenging diagnosis especially in surgical intensive care unit (SICU) patients. The aim of the study was to evaluate for the first time the diagnostic accuracy of the HIT Expert Probability (HEP) score in the early identification of HIT in SICU patients. Methods: The HEP and 4Ts scores were calculated in all patients with suspected HIT during their stay in our SICU. The diagnosis of HIT was finally confirmed (HIT+ group) or excluded (HIT− group) by an independent committee blinded to the HEP and 4Ts score values. The primary outcome was the sensitivity and specificity of a HEP score ≥ 5 for the diagnosis of HIT. The secondary outcome was the area under the ROC curve (AUC) of the HEP and 4Ts scores in the diagnosis of HIT. Results: Respectively 6 and 113 patients were included in the HIT+ and HIT− groups. A HEP score value ≥ 5 had a sensitivity (95% confidence interval (95% CI)) of 1.00 (0.55–1.00), and a specificity (95% CI) of 0.92 (0.86–0.96). The AUC (95% CI) was significantly higher for the HEP score versus for the 4Ts score (0.967 (0.922–1.000) versus 0.707 (0.449–0.965); p = 0.035). Conclusions: A HEP score value < 5 could be helpful to rule out HIT in SICU patients.

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12

Staton, Ashley D., and Jonathon B. Cohen. "A Clinician’s Approach to Double-Hit Lymphoma: Identification, Evaluation, and Management." Journal of Oncology Practice 12, no. 3 (March 2016): 232–38. http://dx.doi.org/10.1200/jop.2015.009647.

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Double-hit lymphomas have concurrent rearrangements of CMYC and BCL2 or occasionally BCL6. Although double-hit lymphomas are a part of the mature B-cell lymphoma lineage, they have an aggressive clinical course that is complicated by an extremely poor response to standard therapy for aggressive non-Hodgkin lymphoma. Overall survival is short for many patients with double-hit lymphomas, which reinforces the importance of identifying appropriate therapies for these patients. Fortunately, recent reports have demonstrated improved outcomes with the use of intensive induction therapies. This article discusses the biology, therapeutic considerations, treatment opinions, possible role of autologous stem-cell transplant, and need for ongoing clinical trials for this subgroup of patients with lymphoma.

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13

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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14

Jumde, Ravindra P., Melissa Guardigni, Robin M. Gierse, Alaa Alhayek, Di Zhu, Zhoor Hamid, Sandra Johannsen, et al. "Hit-optimization using target-directed dynamic combinatorial chemistry: development of inhibitors of the anti-infective target 1-deoxy-d-xylulose-5-phosphate synthase." Chemical Science 12, no. 22 (2021): 7775–85. http://dx.doi.org/10.1039/d1sc00330e.

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Target-directed dynamic combinatorial chemistry was used for hit-identification and subsequent hit-optimization for the anti-infective target 1-deoxy-d-xylulose-5-phosphate synthase resulting in novel inhibitors with low micromolar affinities.

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15

Chen, Rui, Bin Fang, and Patrick Shen-Pei Wang. "Chinese Handwriting Identification Method Based on Keyword Extraction." International Journal of Pattern Recognition and Artificial Intelligence 31, no. 11 (March 31, 2017): 1753004. http://dx.doi.org/10.1142/s0218001417530044.

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Text-independent handwriting identification methods require that features such as texture are extracted from lengthy document image; while text-dependent handwriting identification methods require that the contents of the documents being compared are identical. In order to overcome these confinements, this paper presents a novel Chinese handwriting identification technique. First, Chinese characters are segmented from handwriting document, then keywords are extracted based on matching and voting of local features of character. Then the same-content keywords are used to build training sets, and these training sets of two documents are compared. Because the keywords are similar to signature, the handwriting identification problem is transformed into signature verification problem. Experiments on HIT-MW, HIT-SW and CASIA show this method outperforms many text-independent handwriting identification methods.

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16

Shi, Yong Gang, Hao Wen, Hai Feng Gong, Zi Cun Li, Bin Su, and Ping Sun. "New Algorithm for Engine Oil Identification by Infrared Spectrum." Advanced Materials Research 1081 (December 2014): 353–57. http://dx.doi.org/10.4028/www.scientific.net/amr.1081.353.

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Based on structure and composition characteristics of engine oil, the new algorithm for its Infrared Spectrum (IR) Identification has been put forward. The Hit Quality Index and Related Hit Quality Index are widely used in Infrared Spectrum Identification recently. The two methods don’t take the importance of the variables into consideration and cannot distinguish the unobvious variation in IR spectra. Therefore the diversity weight factor was introduced into the new algorithm to promote its selectivity. The experimental results had shown that the new spectrum similarity evaluation index could distinguish the unobvious spectrum variations and to improve the infrared spectrum identification capability of engine oils.

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17

Balakin, Konstantin, Alexander Kozintsev, Alex Kiselyov, and Nikolay Savchuk. "Rational Design Approaches to Chemical Libraries for Hit Identification." Current Drug Discovery Technologies 3, no. 1 (March 1, 2006): 49–65. http://dx.doi.org/10.2174/157016306776637564.

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18

Volynets, Galyna, Hanna Vyshniakova, Georgiana Nitulescu, George Mihai Nitulescu, Anca Ungurianu, Denisa Margina, Olena Moshynets, et al. "Identification of Novel Antistaphylococcal Hit Compounds Targeting Sortase A." Molecules 26, no. 23 (November 24, 2021): 7095. http://dx.doi.org/10.3390/molecules26237095.

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Staphylococcus aureus (S. aureus) is a causative agent of many hospital- and community-acquired infections with the tendency to develop resistance to all known antibiotics. Therefore, the development of novel antistaphylococcal agents is of urgent need. Sortase A is considered a promising molecular target for the development of antistaphylococcal agents. The main aim of this study was to identify novel sortase A inhibitors. In order to find novel antistaphylococcal agents, we performed phenotypic screening of a library containing 15512 compounds against S. aureus ATCC43300. The molecular docking of hits was performed using the DOCK program and 10 compounds were selected for in vitro enzymatic activity inhibition assay. Two inhibitors were identified, N,N-diethyl-N′-(5-nitro-2-(quinazolin-2-yl)phenyl)propane-1,3-diamine (1) and acridin-9-yl-(1H-benzoimidazol-5-yl)-amine (2), which decrease sortase A activity with IC50 values of 160.3 µM and 207.01 µM, respectively. It was found that compounds 1 and 2 possess antibacterial activity toward 29 tested multidrug resistant S. aureus strains with MIC values ranging from 78.12 to 312.5 mg/L. These compounds can be used for further structural optimization and biological research.

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19

Kotwal, Ashutosh V., Heather K. Gerberich, and Christopher Hays. "Identification of cosmic rays using drift chamber hit timing." Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 506, no. 1-2 (June 2003): 110–18. http://dx.doi.org/10.1016/s0168-9002(03)01371-8.

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20

Jeong, Jinsun, Guehye Kim, Cheol Moon, Hyun Jung Kim, Tae Ho Kim, and Jichan Jang. "Pathogen Box screening for hit identification against Mycobacterium abscessus." PLOS ONE 13, no. 4 (April 26, 2018): e0195595. http://dx.doi.org/10.1371/journal.pone.0195595.

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21

Sakr, Hany, and James R. Cook. "Identification of “Double Hit” Lymphomas Using Updated WHO Criteria." Applied Immunohistochemistry & Molecular Morphology 27, no. 6 (July 2019): 410–15. http://dx.doi.org/10.1097/pai.0000000000000657.

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22

Samarakoon, Lasitha Bhagya, Felicia Chua, Hao Yun Yap, and Edward Choke. "Heparin-induced thrombocytopaenia following abdominal aortic aneurysm repair complicated by treatment failure of rivaroxaban." Proceedings of Singapore Healthcare 29, no. 2 (May 13, 2020): 145–48. http://dx.doi.org/10.1177/2010105820921206.

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Heparin-induced thrombocytopaenia (HIT) is a rare life-threatening complication following exposure to heparin. It is mediated by immune-mediated thrombocytopaenia due to antibody against heparin platelet factor 4 complex. Early identification of the condition and the prompt administration of appropriate treatment are important to prevent morbidity and mortality from HIT. We report a case of HIT associated with open abdominal aortic aneurysm repair causing anterior tibial artery and peroneal artery thrombosis following prophylactic use of unfractionated heparin for prophylaxis of venous thromboembolism. Even though enoxaparin was switched to rivaroxaban after HIT was suspected, our patient unfortunately developed a minor cerebrovascular accident during the hospital stay as a consequence of HIT.

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23

Yoon, Jeong-Joong, Dhruv Chawla, Tanja Paal, Maina Ndungu, Yuhong Du, Serdar Kurtkaya, Aiming Sun, James P. Snyder, and Richard K. Plemper. "High-Throughput Screening—Based Identification of Paramyxovirus Inhibitors." Journal of Biomolecular Screening 13, no. 7 (July 1, 2008): 591–608. http://dx.doi.org/10.1177/1087057108321089.

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Several members of the paramyxovirus family constitute major human pathogens that, collectively, are responsible for major morbidity and mortality worldwide. In an effort to develop novel therapeutics against measles virus (MV), a prominent member of the paramyxovirus family, the authors report a high-throughput screening protocol that uses a nonrecombinant primary MV strain as targets. Implementation of the assay has yielded 60 hit candidates from a 137,500-entry library. Counterscreening and generation of dose-response curves narrows this pool to 35 compounds with active concentrations ≤15.3 µM against the MV-Alaska strain and specificity indices ranging from 36 to >500. Library mining for structural analogs of several confirmed hits combined with retesting of identified candidates reveals a high accuracy of primary hit identification. Eleven of the confirmed hits interfere with viral entry, whereas the remaining 24 compounds target postentry steps of the viral life cycle. Activity testing against selected members of the paramyxovirus family reveals 3 patterns of activity: 1) exclusively MV-specific blockers, 2) inhibitors of MV and related viruses of the same genus, and 3) broader range inhibitors with activity against a different Paramyxovirinae genus. Representatives of the last class may open avenues for the development of broad-range paramyxovirus inhibitors through hit-to-lead chemistry. ( Journal of Biomolecular Screening 2008:591-608)

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24

Morales, John, and Marco Carpio. "Induced Lightning Stroke Identification on Protection Relays." Applied Mechanics and Materials 775 (July 2015): 368–72. http://dx.doi.org/10.4028/www.scientific.net/amm.775.368.

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It is well known that lightning strokes produce mal-operation of transmission line protection relays. Where, protection devices cannot identify correctly between lightning stroke that generates or not permanent faults. Thus, when a flash produces a permanent fault, the protection relay sends a trip order, and the Transmission Line (TL) is disconnected correctly. However, when a lightning stroke does not produce a permanent fault, the protection devices also send the trip order, and the TL is disconnected unnecessary. In this context, these phenomena can produce unnecessary electric power outages, producing damage for the society and economic. Therefore, it is necessary to correctly identify between these lightning stroke signals. Besides that, direct lightning strokes, which hit directly on TLs or transmission towers, have usually been analyzed. However, induced lightning strokes, which hit on ground, have not been considered in previous analyzed. In this paper, in order to identify these induced lightning strokes, an algorithm based on a deterministic focus is proposed.

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25

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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26

Tarnavskiy, S. S., M. V. Protopopov, O. V. Borovykov, A. O. Pryhodko, V. G. Bdzhola, and S. M. Yarmoluk. "Hit identification of FGFR1 inhibitors using receptor-based virtual screening." Biopolymers and Cell 35, no. 2 (April 29, 2019): 143–51. http://dx.doi.org/10.7124/bc.00099f.

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27

Menet, Christel J., Stephen R. Fletcher, Guy Van Lommen, Raphael Geney, Javier Blanc, Koen Smits, Nolwenn Jouannigot, et al. "Triazolopyridines as Selective JAK1 Inhibitors: From Hit Identification to GLPG0634." Journal of Medicinal Chemistry 57, no. 22 (November 17, 2014): 9323–42. http://dx.doi.org/10.1021/jm501262q.

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28

Zugibe, Frederick T., and James T. Costello. "The Jigsaw Puzzle Identification of a Hit-and-Run Automobile." Journal of Forensic Sciences 31, no. 1 (January 1, 1986): 11891J. http://dx.doi.org/10.1520/jfs11891j.

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29

Sikorska, Justyna, Luca Codutti, Lars Skjærven, Bettina Elshorst, Rebeca Saez-Ameneiro, Andrea Angelini, Peter Monecke, and Teresa Carlomagno. "Identification of new hit scaffolds by INPHARMA-guided virtual screening." MedChemComm 6, no. 8 (2015): 1501–7. http://dx.doi.org/10.1039/c5md00116a.

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30

Pellecchia, Maurizio, Barbara Becattini, Kevin J. Crowell, Roberto Fattorusso, Martino Forino, Marco Fragai, Dawoon Jung, Tomas Mustelin, and Lutz Tautz. "NMR-based techniques in the hit identification and optimisation processes." Expert Opinion on Therapeutic Targets 8, no. 6 (December 2004): 597–611. http://dx.doi.org/10.1517/14728222.8.6.597.

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31

Mancini, Federica, M. Yagiz Unver, Walid A. M. Elgaher, Varsha R. Jumde, Alaa Alhayek, Peer Lukat, Jennifer Herrmann, et al. "Protein‐Templated Hit Identification through an Ugi Four‐Component Reaction**." Chemistry – A European Journal 26, no. 64 (September 30, 2020): 14585–93. http://dx.doi.org/10.1002/chem.202002250.

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32

Lee, Ji Young, James M. Krieger, Hongchun Li, and Ivet Bahar. "Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations." Protein Science 29, no. 1 (December 4, 2019): 76–86. http://dx.doi.org/10.1002/pro.3732.

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33

Boscato, Giosuè, and Alessandra Dal Cin. "Damage Assessment of Historic Buildings Hit by Earthquake." Advanced Materials Research 919-921 (April 2014): 1020–26. http://dx.doi.org/10.4028/www.scientific.net/amr.919-921.1020.

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The Church of Gesù and the tower of the Cathedral were stricken and damaged by Emilia-Romagna earthquake sequence of May 2012. This paper presents the procedure for the structural identification of the most widespread types of religious monuments. The dynamic behavior was analyzed using the ambient vibrations test to measure the dynamical properties (mode of vibration, frequencies, displacements and damping ratios) of the constructions using a modal identification of output-only systems. The operational modal analysis OMA has been carried out to identify the modal characteristics through poly-reference Least Square Complex Frequency-domain (pLSFC) estimator. The global structural health monitoring was carried out to define the real dynamic behavior of the damaged constructions that are subjected to different mechanism. These researches are useful for the structural rehabilitation and to define the possible changes in the structural behavior.

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Kang, Hong, Ju Wang, Bin Yao, Sicheng Zhou, and Yang Gong. "Toward safer health care: a review strategy of FDA medical device adverse event database to identify and categorize health information technology related events." JAMIA Open 2, no. 1 (October 12, 2018): 179–86. http://dx.doi.org/10.1093/jamiaopen/ooy042.

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Abstract Introduction Health information technology (HIT) is intended to provide safer and better care to patients. However, poorly designed or implemented HIT poses a key risk to patient safety. It is essential for healthcare providers and researchers to investigate the HIT-related events. Unfortunately, the lack of HIT-related event databases in the community hinders the analysis and management of HIT-related events. Objectives Develop a standardized process for identifying HIT-related events from a Federal Drug Administration (FDA) database in order to create an HIT exclusive database for analysis and learning. Methods The FDA Manufacturer and User Facility Device Experience (MAUDE) database, containing over 7-million reports about medical device malfunctions and problems leading to serious injury or death, was considered as a potential resource to identify HIT-related events. We developed a strategy of identifying and categorizing HIT-related events from the FDA reports through the application of a keyword filter and standardized expert review. Ten percent identified reports were reviewed to measure the consistency among experts and to initialize a database for HIT-related events. Results With the proposed strategy, we initialized an HIT-related event database with over 3500 reports, and updated the estimation of the HIT-related event proportion in the FDA MAUDE database to 0.46∼0.69%, up to 50,000 HIT-related events. Conclusion The proposed strategy for HIT-related event identification holds promise in aiding the understanding, characterization, discovery, and reporting of HIT-related events toward improved patient safety. The analysis of contributing factors under the 8-dimensional sociotechnical model shows that hardware and software, clinical content, and human–computer interface were identified more frequently than the other dimensions.

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Beresini, Maureen H., Yichin Liu, Timothy D. Dawes, Kevin R. Clark, Linda Orren, Stephen Schmidt, Rebecca Turincio, et al. "Small-Molecule Library Subset Screening as an Aid for Accelerating Lead Identification." Journal of Biomolecular Screening 19, no. 5 (February 11, 2014): 758–70. http://dx.doi.org/10.1177/1087057114522515.

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Several small-compound library subsets (14,000 to 56,000) have been established to complement screening of a larger Genentech corporate library (~1,300,000). Two validation sets (~1% of the total library) containing compounds representative of the main library were chosen by selection of plates or individual compounds. Use of these subsets guided selection of assay configuration, validated assay reproducibility, and provided estimates of hit rates expected from our full library. A larger diversity subset representing the scaffold diversity of the full library (3.4% of the total) was designed for screening more challenging targets with limited reagent availability or low-throughput assays. Retrospective analysis of this subset showed hit rates similar to those of the main library while recovering a higher proportion of hit scaffolds. Finally, a property-restricted diversity set called the “in-between library” was established to identify ligand-efficient compounds of molecular size between those typically found in fragment and high-throughput screening libraries. It was screened at fivefold higher concentrations than the main library to facilitate identification of less potent yet ligand-efficient compounds. Taken together, this work underscores the value of generating multiple purpose-focused, diversity-based library subsets that are designed using computational approaches coupled with internal screening data analyses to accelerate the lead discovery process.

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Sparling, Brian A., S. Yi, J. Able, H. Bregman, Erin F. DiMauro, R. S. Foti, H. Gao, et al. "Discovery and hit-to-lead evaluation of piperazine amides as selective, state-dependent NaV1.7 inhibitors." MedChemComm 8, no. 4 (2017): 744–54. http://dx.doi.org/10.1039/c6md00578k.

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Nath, Virendra, Rohini Ahuja, and Vipin Kumar. "Virtual Screening and In Silico Simulation Analysis for Rapid and Efficient Identification of Novel Natural GPR40 Agonist." Letters in Drug Design & Discovery 17, no. 5 (May 18, 2020): 533–46. http://dx.doi.org/10.2174/1570180815666180914162935.

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Background: Diabetes is the foremost health problem worldwide predisposing to increased mortality and morbidity. The available synthetic drugs have serious side effects and thus, emphasize further need to develop effective medication therapy. GPR40 represents an interesting target for developing novel antidiabetic drug. In the current study, searching of potential natural hit candidate as agonist by using structure based computational approach. Methods: The GPR40 agonistic activity of natural compounds was searched by using Maestro through docking and Molecular Dynamics (MD) simulation application. Virtual screening by using IBScreen library of natural compounds was done and the binding modes of newer natural entity(s) were investigated. Further, MD studies of the GPR40 complex with the most promising hit found in this study justified the stability of these complexes. Results: The silicone chip-based approach recognized the most capable six hits and the ADME prediction aided the exploration of their pharmacokinetic potential. In this study, the obtained hit (ZINC70692253) after the use of exhaustive screening having binding energy -107.501 kcal/mol and root mean square deviation of hGPR40-ZINC70692253 is around 3.5 Å in 20 ns of simulation. Conclusion: Successful application of structure-based computational screening gave a novel candidate from Natural Product library for diabetes treatment. So, Natural compounds may tend to cure diabetes with lesser extent of undesirable effects in comparison to synthetic compounds and these novel screened compounds may show a plausible biological response in the hit to lead finding of drug development process. To the best of our knowledge, this is the first example of the successful application of SBVS to discover novel natural hit compounds using hGPR40.

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Mohebbi, Alireza, Fatemeh Sana Askari, Ali Salehnia Sammak, Mohsen Ebrahimi, and Zahra Najafimemar. "Druggability of cavity pockets within SARS-CoV-2 spike glycoprotein and pharmacophore-based drug discovery." Future Virology 16, no. 6 (June 2021): 389–97. http://dx.doi.org/10.2217/fvl-2020-0394.

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Aim: Virus spike glycoprotein of SARS-CoV-2 is a good target for drug discovery. Objective: To examine the potential for druggability of spike protein for pharmacophore-based drug discovery and to investigate the binding affinity of natural products with SARS-CoV-2 spike protein. Methods: Druggable cavities were searched though CavityPlus. A pharmacophore was built and used for hit identification. Autodock Vina was used to evaluate the hits' affinities. 10 chemical derivatives were also made from the chemical backbone to optimize the lead compound. Results: 10 druggable cavities were found within the glycoprotein spike. Only one cavity with the highest score at the binding site was selected for pharmacophore extraction. Hit identification resulted in the identification of 410 hits. Discussion: This study provides a druggable region within viral glycoprotein and a candidate compound to block viral entry.

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Dalebout, Susan D., and Lisa G. Fox. "Identification of the Mismatch Negativity in the Responses of Individual Listeners." Journal of the American Academy of Audiology 11, no. 01 (January 2000): 12–22. http://dx.doi.org/10.1055/s-0042-1748004.

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AbstractThe mismatch negativity (MMN) was recorded from normal adults in three stimulus conditions: two contrast conditions and a control condition in which standard and deviant stimuli were identical. Averaged waveforms were analyzed by examiners blind to the evoking stimulus condition. Hit rates, a false alarm rate, and d values were determined based on the number of MMNs identified in each condition. Hit rates were low and the false alarm rate was relatively high, resulting in unacceptably small d values. The relationship between MMN findings and corresponding behavioral discrimination data for individual listeners was not systematic. Factors that may contribute to ambiguity and error in MMN data analysis are discussed. Abbreviations: ABR = auditory brainstem response, Cz = vertex, Fz = 30 percent of the distance between nasion and inion at the midline, MLR = middle latency response, MMN = mismatch negativity, SNR = signal-to-noise ratio

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Kulkarni, Apoorva M., Vikas Kumar, Shraddha Parate, Gihwan Lee, Sanghwa Yoon, and Keun Woo Lee. "Identification of New KRAS G12D Inhibitors through Computer-Aided Drug Discovery Methods." International Journal of Molecular Sciences 23, no. 3 (January 24, 2022): 1309. http://dx.doi.org/10.3390/ijms23031309.

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Owing to several mutations, the oncogene Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is activated in the majority of cancers, and targeting it has been pharmacologically challenging. In this study, using an in silico approach comprised of pharmacophore modeling, molecular docking, and molecular dynamics simulations, potential KRAS G12D inhibitors were investigated. A ligand-based common feature pharmacophore model was generated to identify the framework necessary for effective KRAS inhibition. The chemical features in the selected pharmacophore model comprised two hydrogen bond donors, one hydrogen bond acceptor, two aromatic rings and one hydrophobic feature. This model was used for screening in excess of 214,000 compounds from InterBioScreen (IBS) and ZINC databases. Eighteen compounds from the IBS and ten from the ZINC database mapped onto the pharmacophore model and were subjected to molecular docking. Molecular docking results highlighted a higher affinity of four hit compounds towards KRAS G12D in comparison to the reference inhibitor, BI-2852. Sequential molecular dynamics (MD) simulation studies revealed all four hit compounds them possess higher KRAS G12D binding free energy and demonstrate stable polar interaction with key residues. Further, Principal Component Analysis (PCA) analysis of the hit compounds in complex with KRAS G12D also indicated stability. Overall, the research undertaken provides strong support for further in vitro testing of these newly identified KRAS G12D inhibitors, particularly Hit1 and Hit2.

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Dürr, Oliver, François Duval, Anthony Nichols, Paul Lang, Annette Brodte, Stephan Heyse, and Dominique Besson. "Robust Hit Identification by Quality Assurance and Multivariate Data Analysis of a High-Content, Cell-Based Assay." Journal of Biomolecular Screening 12, no. 8 (December 2007): 1042–49. http://dx.doi.org/10.1177/1087057107309036.

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Recent technological advances in high-content screening instrumentation have increased its ease of use and throughput, expanding the application of high-content screening to the early stages of drug discovery. However, high-content screens produce complex data sets, presenting a challenge for both extraction and interpretation of meaningful information. This shifts the high-content screening process bottleneck from the experimental to the analytical stage. In this article, the authors discuss different approaches of data analysis, using a phenotypic neurite outgrowth screen as an example. Distance measurements and hierarchical clustering methods lead to a profound understanding of different high-content screening readouts. In addition, the authors introduce a hit selection procedure based on machine learning methods and demonstrate that this method increases the hit verification rate significantly (up to a factor of 5), compared to conventional hit selection based on single readouts only. ( Journal of Biomolecular Screening 2007:1042-1049)

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Weeratna, Jayanie, and Ajith Tennakoon. "Management of The Dead and Missing People in the Easter Bombings in Colombo, Sri Lanka." Journal of Clinical and Health Sciences 6, no. 1(Special) (June 30, 2021): 59. http://dx.doi.org/10.24191/jchs.v6i1(special).13163.

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Identification of the victims is considered as one of the most important initial steps in the management of a mass disaster. Comparison of ante-mortem and post-mortem fingerprints (ridgeology), dental data and DNA profiles have been recognized as primary identification methods for Disaster Victim Identification (DVI). However, facial recognition and personal belongings are the widely used tools of identification in large disasters. A series of bombings hit Sri Lanka on the morning of 21 st of April 2019. In the city of Colombo around 131 people died. Most of the identifications were achieved through visual recognition, with a minor percentage by odontology, genetics and fingerprints. The procedure adopted in the response to the disaster is described in this paper highlighting the importance of advanced preparedness, inter-institutional cooperation, the empathetic approach in caring for the grieving families and the procedure to adopt in visual recognition in DVI.

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Zapata, David, Jose Binongo, Yi Lasanajak, Jane Wei, Bradley G. Leshnower, Edward P. Chen, Jeffrey S. Miller, et al. "Heparin-Induced Thrombocytopenia in Patients Undergoing Valvular and Aortic Surgery: A Modern Assessment of Risk." Innovations: Technology and Techniques in Cardiothoracic and Vascular Surgery 15, no. 3 (March 26, 2020): 229–34. http://dx.doi.org/10.1177/1556984520909799.

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Objective The incidence and outcomes of patients with heparin-induced thrombocytopenia (HIT) are well defined for general cardiac surgical populations. The purpose of this study was to define the outcomes of patients with HIT in a population excluding patients who underwent coronary artery bypass grafting (CABG). Methods The local Society of Thoracic Surgeons cardiac surgical database was queried between January 2008 and May 2017 for patients who underwent either open valvular surgery or aortic surgery. Patients who underwent either isolated or combined CABG procedures were excluded. Cohorts were formed based on the presence or absence of postoperative HIT. Logistic regression models were built to determine the association between postoperative HIT and outcomes, adjusted for both preoperative and intraoperative variables. Results Of the total cohort (8,107 patients), 176 patients (2.2%) developed HIT after surgery. HIT patients experienced an increased incidence of morbidities postoperatively, including reoperation for bleeding, reoperation for cardiac and noncardiac etiologies, postoperative stroke, perioperative myocardial infarction, postoperative sternal infection, postoperative arrhythmia, new-onset renal failure, and dialysis (all with P < 0.01). The unadjusted 30-day mortality was 14.8% in HIT patients vs 4.9% in those without HIT ( P < 0.01). After risk adjustment, reoperation for noncardiac events, renal failure, new dialysis, postoperative stroke, arrhythmia, and sternal wound infection remained significantly elevated in patients who developed postoperative HIT. Conclusions Patients who developed HIT after non-CABG cardiac surgery experienced increased postoperative rates of morbidity and mortality. Early diagnosis and treatment remained mainstays of therapy. Early identification of patients at highest risk should prompt careful risk stratification when possible.

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Ballester, Pedro J., Martina Mangold, Nigel I. Howard, Richard L. Marchese Robinson, Chris Abell, Jochen Blumberger, and John B. O. Mitchell. "Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification." Journal of The Royal Society Interface 9, no. 77 (August 29, 2012): 3196–207. http://dx.doi.org/10.1098/rsif.2012.0569.

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One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor ), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated K i ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification.

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Alnabulsi, Soraya M., and Nizar A. Al-shar’i. "Hit identification of SMYD3 enzyme inhibitors using structure-based pharmacophore modeling." Future Medicinal Chemistry 11, no. 10 (May 2019): 1107–17. http://dx.doi.org/10.4155/fmc-2018-0462.

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Sperandio, O., M. Petitjean, and P. Tuffery. "wwLigCSRre: a 3D ligand-based server for hit identification and optimization." Nucleic Acids Research 37, Web Server (May 8, 2009): W504—W509. http://dx.doi.org/10.1093/nar/gkp324.

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Michel, Julien, and Jonathan W. Essex. "Hit Identification and Binding Mode Predictions by Rigorous Free Energy Simulations." Journal of Medicinal Chemistry 51, no. 21 (November 13, 2008): 6654–64. http://dx.doi.org/10.1021/jm800524s.

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Zhai, Yufeng, Kaisheng Chen, Yang Zhong, Bin Zhou, Edward Ainscow, Ying-Ta Wu, and Yingyao Zhou. "An Automatic Quality Control Pipeline for High-Throughput Screening Hit Identification." Journal of Biomolecular Screening 21, no. 8 (July 10, 2016): 832–41. http://dx.doi.org/10.1177/1087057116654274.

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The correction or removal of signal errors in high-throughput screening (HTS) data is critical to the identification of high-quality lead candidates. Although a number of strategies have been previously developed to correct systematic errors and to remove screening artifacts, they are not universally effective and still require fair amount of human intervention. We introduce a fully automated quality control (QC) pipeline that can correct generic interplate systematic errors and remove intraplate random artifacts. The new pipeline was first applied to ~100 large-scale historical HTS assays; in silico analysis showed auto-QC led to a noticeably stronger structure-activity relationship. The method was further tested in several independent HTS runs, where QC results were sampled for experimental validation. Significantly increased hit confirmation rates were obtained after the QC steps, confirming that the proposed method was effective in enriching true-positive hits. An implementation of the algorithm is available to the screening community.

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Ganzen, Logan, and Yuk Fai Leung. "2095 Drug screening and hit identification for night blindness with zebrafish." Journal of Clinical and Translational Science 2, S1 (June 2018): 11. http://dx.doi.org/10.1017/cts.2018.69.

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OBJECTIVES/SPECIFIC AIMS: Retinitis pigmentosa (RP), also known as night blindness, is an incurable disease which affects ~1 in 4000 individuals globally. Since there are no effective treatment options for RP, the goal of this project is to identify novel drug treatments that can prevent or slow the disease progression. To this end, we optimized a behavioral assay, visual-motor-response (VMR) assay, to investigate rod function (Ganzen et al., ARVO, 2017; Ganzen et al., IJMS, 2017). This was done utilizing a transgenic zebrafish RP model expressing human rhodopsin with the Q344X mutation. In this study, we used this model to perform a proof-of-concept screen for drugs which may improve the vision of the larvae. METHODS/STUDY POPULATION: To screen for beneficial drugs, the SCREEN-WELL® REDOX library was chosen for screening. This library was selected to identify a compound that may alleviate any excessive oxidative stress in the diseased retina. The Q344X zebrafish line suffers from significant rod degeneration by 7 days postfertilization (dpf) and displayed deficits in VMR under scotopic conditions (Ganzen et al., ARVO, 2017). The Q344X larvae were drug treated beginning at 5 dpf at 10 μM. Compounds that were toxic at this concentration were retested at 1 μM. The 5 dpf stage was chosen as most of the rods are intact, and these concentrations were chosen to optimize the drug effect based on similar studies. Hits were identified by assays that provided a robust and reproducible enhancement in the Q344X VMR. The retinae of any drug hits were dissected from larvae crossed with a rod EGFP reporter line and whole-mounted to analyze rod survival via fluorescence. To determine if drug effects were exerted through the retina, eyeless chokh mutant zebrafish were exposed to the drug and tested with the same assay. RESULTS/ANTICIPATED RESULTS: Of the 84 compounds tested, we identified 1 drug that ameliorated the VMR of the Q344X scotopic VMR. Eyeless chokh mutant zebrafish larvae did not exhibit the same VMR when treated with the same drug. Histological analysis suggested increased rod survival in the drug-treated retina of Q344X mutants. DISCUSSION/SIGNIFICANCE OF IMPACT: These results indicate that the vision of the Q344X zebrafish was improved via this beneficial drug treatment. Since eyeless chokh larvae did not respond to the same treatment, the drug likely mediated its positive effects through the Q344X retina, likely by improving rod survival. Together, our results have identified a beneficial drug that may treat RP.

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MacLeod, Kara E., Julia B. Griswold, Lindsay S. Arnold, and David R. Ragland. "Factors associated with hit-and-run pedestrian fatalities and driver identification." Accident Analysis & Prevention 45 (March 2012): 366–72. http://dx.doi.org/10.1016/j.aap.2011.08.001.

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