443 results on '"Ekins, S"'
Search Results
2. CATMoS: Collaborative Acute Toxicity Modeling Suite
- Author
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Mansouri, K, Karmaus, A, Fitzpatrick, J, Patlewicz, G, Pradeep, P, Alberga, D, Alepee, N, Allen, T, Allen, D, Alves, V, Andrade, C, Auernhammer, T, Ballabio, D, Bell, S, Benfenati, E, Bhattacharya, S, Bastos, J, Boyd, S, Brown, J, Capuzzi, S, Chushak, Y, Ciallella, H, Clark, A, Consonni, V, Daga, P, Ekins, S, Farag, S, Fedorov, M, Fourches, D, Gadaleta, D, Gao, F, Gearhart, J, Goh, G, Goodman, J, Grisoni, F, Grulke, C, Hartung, T, Hirn, M, Karpov, P, Korotcov, A, Lavado, G, Lawless, M, Li, X, Luechtefeld, T, Lunghini, F, Mangiatordi, G, Marcou, G, Marsh, D, Martin, T, Mauri, A, Muratov, E, Myatt, G, Nguyen, D, Nicolotti, O, Note, R, Pande, P, Parks, A, Peryea, T, Polash, A, Rallo, R, Roncaglioni, A, Rowlands, C, Ruiz, P, Russo, D, Sayed, A, Sayre, R, Sheils, T, Siegel, C, Silva, A, Simeonov, A, Sosnin, S, Southall, N, Strickland, J, Tang, Y, Teppen, B, Tetko, I, Thomas, D, Tkachenko, V, Todeschini, R, Toma, C, Tripodi, I, Trisciuzzi, D, Tropsha, A, Varnek, A, Vukovic, K, Wang, Z, Wang, L, Waters, K, Wedlake, A, Wijeyesakere, S, Wilson, D, Xiao, Z, Yang, H, Zahoranszky-Kohalmi, G, Zakharov, A, Zhang, F, Zhang, Z, Zhao, T, Zhu, H, Zorn, K, Casey, W, Kleinstreuer, N, Mansouri, Kamel, Karmaus, Agnes L, Fitzpatrick, Jeremy, Patlewicz, Grace, Pradeep, Prachi, Alberga, Domenico, Alepee, Nathalie, Allen, Timothy E H, Allen, Dave, Alves, Vinicius M, Andrade, Carolina H, Auernhammer, Tyler R, Ballabio, Davide, Bell, Shannon, Benfenati, Emilio, Bhattacharya, Sudin, Bastos, Joyce V, Boyd, Stephen, Brown, J B, Capuzzi, Stephen J, Chushak, Yaroslav, Ciallella, Heather, Clark, Alex M, Consonni, Viviana, Daga, Pankaj R, Ekins, Sean, Farag, Sherif, Fedorov, Maxim, Fourches, Denis, Gadaleta, Domenico, Gao, Feng, Gearhart, Jeffery M, Goh, Garett, Goodman, Jonathan M, Grisoni, Francesca, Grulke, Christopher M, Hartung, Thomas, Hirn, Matthew, Karpov, Pavel, Korotcov, Alexandru, Lavado, Giovanna J, Lawless, Michael, Li, Xinhao, Luechtefeld, Thomas, Lunghini, Filippo, Mangiatordi, Giuseppe F, Marcou, Gilles, Marsh, Dan, Martin, Todd, Mauri, Andrea, Muratov, Eugene N, Myatt, Glenn J, Nguyen, Dac-Trung, Nicolotti, Orazio, Note, Reine, Pande, Paritosh, Parks, Amanda K, Peryea, Tyler, Polash, Ahsan H, Rallo, Robert, Roncaglioni, Alessandra, Rowlands, Craig, Ruiz, Patricia, Russo, Daniel P, Sayed, Ahmed, Sayre, Risa, Sheils, Timothy, Siegel, Charles, Silva, Arthur C, Simeonov, Anton, Sosnin, Sergey, Southall, Noel, Strickland, Judy, Tang, Yun, Teppen, Brian, Tetko, Igor V, Thomas, Dennis, Tkachenko, Valery, Todeschini, Roberto, Toma, Cosimo, Tripodi, Ignacio, Trisciuzzi, Daniela, Tropsha, Alexander, Varnek, Alexandre, Vukovic, Kristijan, Wang, Zhongyu, Wang, Liguo, Waters, Katrina M, Wedlake, Andrew J, Wijeyesakere, Sanjeeva J, Wilson, Dan, Xiao, Zijun, Yang, Hongbin, Zahoranszky-Kohalmi, Gergely, Zakharov, Alexey V, Zhang, Fagen F, Zhang, Zhen, Zhao, Tongan, Zhu, Hao, Zorn, Kimberley M, Casey, Warren, Kleinstreuer, Nicole C, Mansouri, K, Karmaus, A, Fitzpatrick, J, Patlewicz, G, Pradeep, P, Alberga, D, Alepee, N, Allen, T, Allen, D, Alves, V, Andrade, C, Auernhammer, T, Ballabio, D, Bell, S, Benfenati, E, Bhattacharya, S, Bastos, J, Boyd, S, Brown, J, Capuzzi, S, Chushak, Y, Ciallella, H, Clark, A, Consonni, V, Daga, P, Ekins, S, Farag, S, Fedorov, M, Fourches, D, Gadaleta, D, Gao, F, Gearhart, J, Goh, G, Goodman, J, Grisoni, F, Grulke, C, Hartung, T, Hirn, M, Karpov, P, Korotcov, A, Lavado, G, Lawless, M, Li, X, Luechtefeld, T, Lunghini, F, Mangiatordi, G, Marcou, G, Marsh, D, Martin, T, Mauri, A, Muratov, E, Myatt, G, Nguyen, D, Nicolotti, O, Note, R, Pande, P, Parks, A, Peryea, T, Polash, A, Rallo, R, Roncaglioni, A, Rowlands, C, Ruiz, P, Russo, D, Sayed, A, Sayre, R, Sheils, T, Siegel, C, Silva, A, Simeonov, A, Sosnin, S, Southall, N, Strickland, J, Tang, Y, Teppen, B, Tetko, I, Thomas, D, Tkachenko, V, Todeschini, R, Toma, C, Tripodi, I, Trisciuzzi, D, Tropsha, A, Varnek, A, Vukovic, K, Wang, Z, Wang, L, Waters, K, Wedlake, A, Wijeyesakere, S, Wilson, D, Xiao, Z, Yang, H, Zahoranszky-Kohalmi, G, Zakharov, A, Zhang, F, Zhang, Z, Zhao, T, Zhu, H, Zorn, K, Casey, W, Kleinstreuer, N, Mansouri, Kamel, Karmaus, Agnes L, Fitzpatrick, Jeremy, Patlewicz, Grace, Pradeep, Prachi, Alberga, Domenico, Alepee, Nathalie, Allen, Timothy E H, Allen, Dave, Alves, Vinicius M, Andrade, Carolina H, Auernhammer, Tyler R, Ballabio, Davide, Bell, Shannon, Benfenati, Emilio, Bhattacharya, Sudin, Bastos, Joyce V, Boyd, Stephen, Brown, J B, Capuzzi, Stephen J, Chushak, Yaroslav, Ciallella, Heather, Clark, Alex M, Consonni, Viviana, Daga, Pankaj R, Ekins, Sean, Farag, Sherif, Fedorov, Maxim, Fourches, Denis, Gadaleta, Domenico, Gao, Feng, Gearhart, Jeffery M, Goh, Garett, Goodman, Jonathan M, Grisoni, Francesca, Grulke, Christopher M, Hartung, Thomas, Hirn, Matthew, Karpov, Pavel, Korotcov, Alexandru, Lavado, Giovanna J, Lawless, Michael, Li, Xinhao, Luechtefeld, Thomas, Lunghini, Filippo, Mangiatordi, Giuseppe F, Marcou, Gilles, Marsh, Dan, Martin, Todd, Mauri, Andrea, Muratov, Eugene N, Myatt, Glenn J, Nguyen, Dac-Trung, Nicolotti, Orazio, Note, Reine, Pande, Paritosh, Parks, Amanda K, Peryea, Tyler, Polash, Ahsan H, Rallo, Robert, Roncaglioni, Alessandra, Rowlands, Craig, Ruiz, Patricia, Russo, Daniel P, Sayed, Ahmed, Sayre, Risa, Sheils, Timothy, Siegel, Charles, Silva, Arthur C, Simeonov, Anton, Sosnin, Sergey, Southall, Noel, Strickland, Judy, Tang, Yun, Teppen, Brian, Tetko, Igor V, Thomas, Dennis, Tkachenko, Valery, Todeschini, Roberto, Toma, Cosimo, Tripodi, Ignacio, Trisciuzzi, Daniela, Tropsha, Alexander, Varnek, Alexandre, Vukovic, Kristijan, Wang, Zhongyu, Wang, Liguo, Waters, Katrina M, Wedlake, Andrew J, Wijeyesakere, Sanjeeva J, Wilson, Dan, Xiao, Zijun, Yang, Hongbin, Zahoranszky-Kohalmi, Gergely, Zakharov, Alexey V, Zhang, Fagen F, Zhang, Zhen, Zhao, Tongan, Zhu, Hao, Zorn, Kimberley M, Casey, Warren, and Kleinstreuer, Nicole C
- Abstract
Background: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silica models built using existing data facilitate rapid acute tox- icity predictions without using animals. Objkctivks: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organ- ized an international collaboration to develop in silica models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50 ≤ 50 mg/kg)], and nontoxic chemicals (LD50 > 2,000 mg/kg). Mkthods: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. Results: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in viva results. Discussion: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in viva rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemica
- Published
- 2021
3. Quantum Machine Learning for Drug Discovery
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Daniel H. Foil, Gawriljuk Vo, ekins s, Lane Tr, Kimberley M. Zorn, Kushal Batra, and Eni Minerali
- Subjects
Quantum machine learning ,business.industry ,Drug discovery ,Computer science ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Machine learning ,computer.software_genre ,Support vector machine ,Cheminformatics ,Molecular descriptor ,Classifier (linguistics) ,Artificial intelligence ,business ,computer ,Quantum computer - Abstract
The growing public and private datasets focused on small molecules screened against biological targets or whole organisms 1 provides a wealth of drug discovery relevant data. Increasingly this is used to create machine learning models which can be used for enabling target-based design 2-4, predict on- or off-target effects and create scoring functions 5,6. This is matched by the availability of machine learning algorithms such as Support Vector Machines (SVM) and Deep Neural Networks (DNN) that are computationally expensive to perform on very large datasets and thousands of molecular descriptors. Quantum computer (QC) algorithms have been proposed to offer an approach to accelerate quantum machine learning over classical computer (CC) algorithms, however with significant limitations. In the case of cheminformatics, one of the challenges to overcome is the need for compression of large numbers of molecular descriptors for use on QC. Here we show how to achieve compression with datasets using hundreds of molecules (SARS-CoV-2) to hundreds of thousands (whole cell screening datasets for plague and M. tuberculosis) with SVM and data re-uploading classifier (a DNN equivalent algorithm) on a QC benchmarked against CC and hybrid approaches. This illustrates a quantum advantage for drug discovery to build upon in future.
- Published
- 2020
4. In vivo activity of pyrimidine-dispirotripiperaziniumin in the male guinea pig model of genital herpes
- Author
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Novoselova Ea, Alimbarova Lm, LepioshkinAY, Makarov Va, Ekins S, and Monakhova Ns
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Infectivity ,business.industry ,Therapeutic effect ,Heparan sulfate ,Pharmacology ,medicine.disease_cause ,In vitro ,Guinea pig ,Lesion ,chemistry.chemical_compound ,Herpes simplex virus ,chemistry ,In vivo ,medicine ,medicine.symptom ,business - Abstract
Herpes Simplex Virus (HSV-2) is a risk factor in the transmission of human immunodeficiency virus. While treatments exist for HSV they are either not completely effective or have a single target. We have described a novel pyrimidyl-di(diazaspiroalkane) derivative called 3,3’-(2-methyl-5-nitropyrimidine-4,6-diyl)-3,12-bis-6,9-diazadiazoniadispiro [5.2.5.2]hexadecane tetrachloride dihydrochloride (PDSTP) that targets heparan sulfate on host cells and has broad spectrum antiviral activity and lacks cytotoxicity. In previous studies we have confirmed the antiviral activity in vitro and now present the results of in vivo testing. We demonstrated that 10% ointment or 10% gel containing PDSTP administered topically or injected subcutaneously (twice daily for 5 days) has a therapeutic effect in the guinea pig model of genital herpes induced by HSV-2. PDSTP reduces symptom intensity, time of lesion resolution, mean disease duration and infectivity of HSV-2. The strongest effect was observed for the PDSTP solution administered parenterally, while the minimum effect was shown in the experiments when 10% gel was applied onto the lesion foci. Further experiments were performed which showed all the dosage forms had efficacy which was dependent on treatment initiation time. PDSTP performed comparably well against clinical symptoms versus acyclovir. Both PDSTP and acyclovir have different mechanisms so future work to study the effect of combination treatment is warranted.
- Published
- 2020
5. Computational Modeling to Accelerate the Identification of Substrates and Inhibitors for Transporters That Affect Drug Disposition
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Ekins, S, Polli, J E, Swaan, P W, and Wright, S H
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- 2012
6. G482 Ring the alarm; changing our approach to high-risk safeguarding in the children’s emergency department
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Hannah, R, primary, Brain, I, additional, Ekins, S, additional, Howsam, F, additional, and Walton, E, additional
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- 2020
- Full Text
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7. In silico pharmacology for drug discovery: applications to targets and beyond
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Ekins, S, Mestres, J, and Testa, B
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- 2007
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8. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling
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Ekins, S, Mestres, J, and Testa, B
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- 2007
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9. CTP synthetase and panthotenate kinase: two new tools for a multi-targeting strategy against Mycobacterium tuberculosis
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Chiarelli, LR, Esposito, M, Orena, BS, Mori, G, Gosetti, F, Manfredi, M, Ekins, S, Marengo, E, Ballell-Pages, L, Mikušová, K, Riccardi, G, Pasca, MR, Chiarelli, L, Esposito, M, Orena, B, Mori, G, Gosetti, F, Manfredi, M, Ekins, S, Marengo, E, Ballell-Pages, L, Mikušová, K, Riccardi, G, and Pasca, M
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CHIM/01 - CHIMICA ANALITICA ,CTP synthetase, panthotenate kinase, Mycobacterium tuberculosis, LC-MS - Published
- 2017
10. Mycobacterium tuberculosis CTP synthetase and pantothenate kinase: two promising targets for the development of multitargeting drugs
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Chiarelli, LR, Esposito, M, Orena, BS, Mori, G, Buttari, N, Degiacomi, G, Gosetti, F, Manfredi, M, Ekins, S, Mikušová, K, Bellinzoni, M, Manganelli, R, Marengo, E, Ballell-Pages, L, Riccardi, G, Pasca,MR, Chiarelli, L, Esposito, M, Orena, B, Mori, G, Buttari, N, Degiacomi, G, Gosetti, F, Manfredi, M, Ekins, S, Mikušová, K, Bellinzoni, M, Manganelli, R, Marengo, E, Ballell-Pages, L, Riccardi, G, and Pasca, M
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CHIM/01 - CHIMICA ANALITICA ,Mycobacterium tuberculosis, pantothenate kinase, SWATH-MS - Published
- 2016
11. A multitarget approach to drug discovery inhibiting Mycobacterium tuberculosis PyrG and PanK
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Chiarelli, L, Mori, G, Orena, B, Esposito, M, Lane, T, De Jesus Lopes Ribeiro, A, Degiacomi, G, Zemanová, J, Szádocka, S, Huszár, S, Palčeková, Z, Manfredi, M, Gosetti, F, Lelièvre, J, Ballell, L, Kazakova, E, Makarov, V, Marengo, E, Mikusova, K, Cole, S, Riccardi, G, Ekins, S, Pasca, M, Chiarelli, Laurent R., Mori, Giorgia, Orena, Beatrice Silvia, Esposito, Marta, Lane, Thomas, De Jesus Lopes Ribeiro, Ana Luisa, Degiacomi, Giulia, Zemanová, Júlia, Szádocka, Sára, Huszár, Stanislav, Palčeková, Zuzana, Manfredi, Marcello, Gosetti, Fabio, Lelièvre, Joël, Ballell, Lluis, Kazakova, Elena, Makarov, Vadim, Marengo, Emilio, Mikusova, Katarina, Cole, Stewart T., Riccardi, Giovanna, Ekins, Sean, Pasca, Maria Rosalia, Chiarelli, L, Mori, G, Orena, B, Esposito, M, Lane, T, De Jesus Lopes Ribeiro, A, Degiacomi, G, Zemanová, J, Szádocka, S, Huszár, S, Palčeková, Z, Manfredi, M, Gosetti, F, Lelièvre, J, Ballell, L, Kazakova, E, Makarov, V, Marengo, E, Mikusova, K, Cole, S, Riccardi, G, Ekins, S, Pasca, M, Chiarelli, Laurent R., Mori, Giorgia, Orena, Beatrice Silvia, Esposito, Marta, Lane, Thomas, De Jesus Lopes Ribeiro, Ana Luisa, Degiacomi, Giulia, Zemanová, Júlia, Szádocka, Sára, Huszár, Stanislav, Palčeková, Zuzana, Manfredi, Marcello, Gosetti, Fabio, Lelièvre, Joël, Ballell, Lluis, Kazakova, Elena, Makarov, Vadim, Marengo, Emilio, Mikusova, Katarina, Cole, Stewart T., Riccardi, Giovanna, Ekins, Sean, and Pasca, Maria Rosalia
- Abstract
Mycobacterium tuberculosis, the etiological agent of the infectious disease tuberculosis, kills approximately 1.5 million people annually, while the spread of multidrug-resistant strains is of great global concern. Thus, continuous efforts to identify new antitubercular drugs as well as novel targets are crucial. Recently, two prodrugs activated by the monooxygenase EthA, 7947882 and 7904688, which target the CTP synthetase PyrG, were identified and characterized. In this work, microbiological, biochemical, and in silico methodologies were used to demonstrate that both prodrugs possess a second target, the pantothenate kinase PanK. This enzyme is involved in coenzyme A biosynthesis, an essential pathway for M. tuberculosis growth. Moreover, compound 11426026, the active metabolite of 7947882, was demonstrated to directly inhibit PanK, as well. In an independent screen of a compound library against PyrG, two additional inhibitors were also found to be active against PanK. In conclusion, these direct PyrG and PanK inhibitors can be considered as leads for multitarget antitubercular drugs and these two enzymes could be employed as a "double-tool" in order to find additional hit compounds.
- Published
- 2018
12. CTP synthetase and panthotenate kinase: two new tools for a multi-targeting strategy against Mycobacterium tuberculosis
- Author
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Chiarelli, L, Esposito, M, Orena, B, Mori, G, Gosetti, F, Manfredi, M, Ekins, S, Marengo, E, Ballell-Pages, L, Mikušová, K, Riccardi, G, Pasca, M, Chiarelli, LR, Orena, BS, Pasca, MR, Chiarelli, L, Esposito, M, Orena, B, Mori, G, Gosetti, F, Manfredi, M, Ekins, S, Marengo, E, Ballell-Pages, L, Mikušová, K, Riccardi, G, Pasca, M, Chiarelli, LR, Orena, BS, and Pasca, MR
- Published
- 2017
13. CARVEDILOL AS A POTENTIAL CHEMOTHERAPEUTIC AND CANCER PREVENTIVE AGENT THROUGH ITS INHIBITION OF PARP-1.
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MCMURTRAY, A. M., JAIN, S., EKINS, S., and TAMRAZIAN, E.
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CARVEDILOL ,MUTAGENESIS ,TELANGIECTASIA ,ATAXIA ,CLINICAL trials - Abstract
Carvedilol is an established anti-hypertensive medication used as one of the cornerstones of congestive heart failure. In addition to its cardiac remodeling properties, recent interest has been shown in the field of cancer mutagenesis. Inhibition of various proteins involved in proliferation pathways in cancer formation has shown potential therapeutic applications in protecting against apoptosis. Various clinical trials have recently been employed to study potential inhibitors of poly (ADP-ribose) polymerase 1, a well-known protein involved in cancer mutagenesis. Our study suggests a potential inhibitory interaction with polymerase 1and Carvedilol. By using virtual screening target software, we hope to identify a potential pharmacological interaction between Carvedilol and various well known cancer genes, which can serve as possible therapeutic targets and potential chemo-preventative agents. We used PyRx, which is a virtual screening and docking software program, to screen proteins known to be involved in DNA repair, cancer prevention, and programmed cell death pathways and measure their binding affinities with Carvedilol. Among the various proteins tested with our virtual screening program, Carvedilol showed the highest binding affinity of -8.7 kcal/mol, to polymerase 1as well as with the receptor tyrosineprotein kinase erb-2, (HER2/neu), often found frequently in breast cancer (-8.3 kcal/mol) and also with the serine protein kinase ATM protein, involved in Ataxia Telangiectasia with a high binding affinity of -8.8 kcal/mol. Although numerous anti-cancer mechanisms have been postulated and appropriate pharmaceutical agents have been designed which have decreased mortality, unwanted toxicity and cost has remained a limiting factor. Recent studies have focused on particular cancer mutagenesis pathways such as the role of polymerase 1 and proliferation in certain cancers. Our studies suggest a significant binding and inhibition of polymerase 1 with Carvedilol. This presents a novel and potential therapeutic role as a cost effective and readily available cancer treatment as well as possible chemo-preventative medication in certain cancers with little or no effective treatments. [ABSTRACT FROM AUTHOR]
- Published
- 2018
14. Mycobacterium tuberculosis CTP synthetase and pantothenate kinase: two promising targets for the development of multitargeting drugs
- Author
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Chiarelli, L, Esposito, M, Orena, B, Mori, G, Buttari, N, Degiacomi, G, Gosetti, F, Manfredi, M, Ekins, S, Mikušová, K, Bellinzoni, M, Manganelli, R, Marengo, E, Ballell-Pages, L, Riccardi, G, Pasca, M, Chiarelli, LR, Orena, BS, Pasca,MR, Chiarelli, L, Esposito, M, Orena, B, Mori, G, Buttari, N, Degiacomi, G, Gosetti, F, Manfredi, M, Ekins, S, Mikušová, K, Bellinzoni, M, Manganelli, R, Marengo, E, Ballell-Pages, L, Riccardi, G, Pasca, M, Chiarelli, LR, Orena, BS, and Pasca,MR
- Published
- 2016
15. G55(P) Common clinical features in children with dengue shock syndrome in Myanmar: A case series
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Ekins, S, primary, Halbert, J, additional, and Myint, AA, additional
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- 2016
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16. The Tyndall Decarbonisation Scenarios Part II: scenarios for a 60% CO2 reduction in the UK
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Alice Bows-Larkin, Kevin Anderson, P Agnolucci, P Ekins, S Shackley, Sarah Mander
- Abstract
This paper describes the Tyndall decarbonisation scenarios, the first to take account of CO2 emissions from the whole of the UK's energy system, including emissions from international shipping and aviation. It builds on Part I, which outlined the backcasting methodology developed to generate the scenarios. The five scenarios produced through this process articulate alternative vision of a substantially decarbonised society in 2050, ranging from a halving of energy consumption from current levels to a near doubling. This work demonstrates that a 60% reduction in the UK's CO2 emissions is achievable, even when all CO2 sources are taken into account. The impacts and consequences of the scenarios were assessed by means of a multi-criteria framework which cautions us that the high energy demand scenarios will have a large impact on broader sustainability criteria.
- Published
- 2008
17. The Tyndall Decarbonisation Scenarios Part I: development of a backcasting methodology with stakeholder participation
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Alice Bows-Larkin, Kevin Anderson, P Agnolucci, P Ekins, S Shackley, Sarah Mander
- Abstract
The Tyndall decarbonisation scenarios project has outlined alternative pathways whereby a 60% reduction in CO2 emissions from 1990 levels by 2050, a goal adopted by the UK Government, can be achieved. This paper, Part I of a two part paper, describes the methodology used to develop the scenarios and outlines the motivations for the project. The study utilised a backcasting approach, applied in three phases. In phase one, a set of credible and consistent end-points that described a substantially decarbonised energy system in 2050 were generated and reviewed by stakeholders. In phase two, pathways were developed to achieve the transition to the desired end-point. The impacts of the scenarios were assessed in phase three, by means of a deliberative multi-criteria assessment framework. The scenarios to emerge from this process are elaborated in Part II, and conclusions drawn in relation to the feasibility of achieving the 60% target.
- Published
- 2008
18. Cross-reactivity studies and predictive modeling of “Bath Salts” and other amphetamine-type stimulants with amphetamine screening immunoassays
- Author
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Petrie, M., primary, Lynch, K. L., additional, Ekins, S., additional, Chang, J. S., additional, Goetz, R. J., additional, Wu, A. H. B., additional, and Krasowski, M. D., additional
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- 2013
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19. Towards a new age of virtual ADME/TOX and multidimensional drug discovery
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UCL, Ekins, S, Boulanger, Bruno, Swaan, PW, Hupcey, MAZ, UCL, Ekins, S, Boulanger, Bruno, Swaan, PW, and Hupcey, MAZ
- Abstract
With the continual pressure to ensure follow-up molecules to billion dollar blockbuster drugs, there is hurdle in profitability and growth for pharmaceutical companies in the next decades. With each success and failure we increasingly appreciate that key to the success of synthesized molecules through the research and development process is the possession of drug-like properties. These properties include an adequate bioactivity as well as adequate solubility, an ability to cross critical membranes (intestinal and sometimes blood-brain barrier), reasonable metabolic stability and of course safety in humans. Dependent on the therapeutic area being investigated it might also be desirable to void certain enzymes or transporters to circumvent potential drug-drug interactions. It may also be important to limit the induction of these same proteins that can result in further toxicities. We have clearly moved the assessment of in vitro absorption, distribution, metabolism, excretion and toxicity (ADME/TOX) parameters much earlier in the discovery organization than decade ago with the inclusion of higher throughput systems. We are also now faced with huge amounts of ADME/TOX data for each molecule that need interpretation and also provide valuable resource for generating predictive computational models for future drug discovery. The present review aims to show what tools exist today for visualizing and modeling ADME/TOX data, what tools need to be developed, and how both the present and future tools are valuable for virtual filtering using ADME/TOX and bioactivity properties in parallel as viable addition to present practices.
- Published
- 2002
20. Treatment Patterns and Asthma Control Among US Allergy and Pulmonary Community Practices: Results of the CHARIOT Study
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MARCUS, P, primary, ARNOLD, R, additional, EKINS, S, additional, SACCO, P, additional, MASSANARI, M, additional, DONOHUE, J, additional, and BUKSTEIN, D, additional
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- 2008
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21. Future directions for drug transporter modelling
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Ekins, S., primary, Ecker, G. F., additional, Chiba, P., additional, and Swaan, P. W., additional
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- 2007
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22. Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms
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Ekins, S., primary, Bugrim, A., additional, Brovold, L., additional, Kirillov, E., additional, Nikolsky, Y., additional, Rakhmatulin, E., additional, Sorokina, S., additional, Ryabov, A., additional, Serebryiskaya, T., additional, Melnikov, A., additional, Metz, J., additional, and Nikolskaya, T., additional
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- 2006
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23. Techniques: Application of systems biology to absorption, distribution, metabolism, excretion and toxicity
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EKINS, S, primary, NIKOLSKY, Y, additional, and NIKOLSKAYA, T, additional
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- 2005
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24. PXR and the regulation of apoA1 and HDL-cholesterol in rodents
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BACHMANN, K, primary, PATEL, H, additional, BATAYNEH, Z, additional, SLAMA, J, additional, WHITE, D, additional, POSEY, J, additional, EKINS, S, additional, GOLD, D, additional, and SAMBUCETTI, L, additional
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- 2004
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25. In silico approaches to predicting drug metabolism, toxicology and beyond
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Ekins, S., primary
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- 2003
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26. Characterization of transgenic mouse strains using six human hepatic cytochrome P450 probe substrates
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Mankowski, D. C., primary, Lawton, M. P., additional, and Ekins, S., additional
- Published
- 2000
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27. A retrospective randomized study of asthma control in the US: results of the CHARIOT study.
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Marcus P, Arnold RJG, Ekins S, Sacco P, Massanari M, Stanley Young S, Donohue J, Bukstein D, CHARIOT Study Investigators, Marcus, Philip, Arnold, Renée J G, Ekins, Sean, Sacco, Patricia, Massanari, Marc, Stanley Young, S, Donohue, James, and Bukstein, Don
- Abstract
Background: The third version of the National Asthma Education and Prevention Program (NAEPP) Expert Panel Report (EPR-3): Guidelines on the Diagnosis and Management of Asthma emphasizes the need to use asthma control rather than patient severity to base adjustments to treatment and ultimately improve patient outcomes. The objectives of the current study were to assess control of patients with moderate-to-severe asthma, examine the natural history of the disease, practice patterns and resource utilization in specialty community practices according to recently reviewed NAEPP guidelines.Research Design and Methods: This analysis represents a retrospective, multicenter, randomized study of 1009 patient charts in sixty United States allergy and pulmonary medicine community practices. The proportion of patients with controlled and uncontrolled asthma over 12 months, prevalence and characteristics of atopy, past asthma history, pulmonary function, medications and treatment patterns, patient and clinical practice characteristics were analyzed.Main Outcome Measures: The primary outcome of interest was asthma control.Results: A total of 365 male and 644 female patients with moderate-to-severe persistent asthma (mean 43.2 +/- 17.1 years) were enrolled. 81.9% of patients were uncontrolled according to recent NAEPP guidelines. Importantly, a greater percentage of patients with moderate asthma vs. severe persistent asthma were uncontrolled (p < 0.0114). Atopy was detected in 92% of patients. Patients with early onset of asthma were associated with control (p < 0.0433). Atopic symptoms, such as allergic rhinitis (p < 0.0130) and rhinosinusitis (p < 0.0476), were associated with uncontrolled asthma. Uncontrolled patients were also associated with more medications (a mean of 4.05 +/- 1.87 medications) than were controlled patients (a mean of 3.40 +/- 1.37 medications (p < 0.0001), although the temporal relationship of this association was not recorded. Limitations may have included patient and/or study site selection bias and difficulty in the process of operationalizing the definitions of control and disease severity. Since the current study only examined patients from specialty practices, the results may not be generalizable to the overall asthma population.Conclusions: Greater than 80% of asthma patients from specialty practices were uncontrolled with regard to asthma symptoms. Atopic symptoms, such as allergic rhinitis and rhinosinusitis, in addition to a greater number of medications, were associated with uncontrolled asthma. Moreover, patients designated as having asthma of moderate severity were associated with being uncontrolled more than were those with severe asthma (p < 0.0114), which suggests that the former population may not have received adequate assessment of impairment or risk, with subsequent changes in treatment for control of symptoms. [ABSTRACT FROM AUTHOR]- Published
- 2008
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28. In silico ADME/Tox: the state of the art
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Ekins, S. and Rose, J.
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- 2002
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29. Three-Dimensional Quantitative Structure-Permeability Relationship Analysis for a Series of Inhibitors of Rhinovirus Replication
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Ekins, S., Durst, G. L., Stratford, R. E., Thorner, D. A., Lewis, R., Loncharich, R. J., and Wikel, J. H.
- Abstract
Multiple three-dimensional quantitative structure−activity relationship (3D-QSAR) approaches were applied to predicting passive Caco-2 permeability for a series of 28 inhibitors of rhinovirus replication. Catalyst, genetic function approximation (GFA) with MS-WHIM descriptors, CoMFA, and VolSurf were all used for generating 3D-quantitative structure permeability relationships utilizing a training set of 19 molecules. Each of these approaches was then compared using a test set of nine molecules not present in the training set. Statistical parameters for the test set predictions (r2 and leave-one-out q2) were used to compare the models. It was found that the Catalyst pharmacophore model was the most predictive (test set of predicted versus observed permeability, r2 = 0.94). This model consisted of a hydrogen bond acceptor, hydrogen bond donor, and ring aromatic feature with a training set correlation of r2 = 0.83. The CoMFA model consisted of three components with an r2 value of 0.96 and produced good predictions for the test set (r2 = 0.84). VolSurf resulted in an r2 value of 0.76 and good predictions for the test set (r2 = 0.83). Test set predictions with GFA/WHIM descriptors (r2 = 0.46) were inferior when compared with the Catalyst, CoMFA, and VolSurf model predictions in this evaluation. In summary it would appear that the 3D techniques have considerable value in predicting passive permeability for a congeneric series of molecules, representing a valuable asset for drug discovery.
- Published
- 2001
30. Application of in silico approaches to predicting drug-drug interactions
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Ekins, S. and Wrighton, S. A.
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- 2001
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31. Progress in predicting human ADME parameters in silico
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Ekins, S., Waller, C. L., Swaan, P. W., Cruciani, G., Wrighton, S. A., and Wikel, J. H.
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- 2000
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32. Present and future in vitro approaches for drug metabolism
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Ekins, S., Ring, B. J., Grace, J., McRobie-Belle, D. J., and Wrighton, S. A.
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- 2000
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33. Accessing, using, and creating chemical property databases for computational toxicology modeling
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Williams, Aj, Ekins, S., Ola Spjuth, and Willighagen, El
34. Illustrating and homology modeling the proteins of the Zika virus
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Ekins S, Liebler J, Bj, Neves, Wg, Lewis, Coffee M, Bienstock R, Christopher Southan, and Ch, Andrade
35. Free online resources enabling crowd-sourced drug discovery
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Antony Williams, Tkachenko, V., Lipinski, C., Tropsha, A., and Ekins, S.
36. CATMoS: Collaborative Acute Toxicity Modeling Suite
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Tyler Peryea, Ahsan Habib Polash, Alessandra Roncaglioni, Daniel M. Wilson, Warren Casey, Patricia Ruiz, Nathalie Alépée, Sherif Farag, Giovanna J. Lavado, Kimberley M. Zorn, Alexey V. Zakharov, Davide Ballabio, Katrina M. Waters, Risa Sayre, Giuseppe Felice Mangiatordi, Orazio Nicolotti, Nicole Kleinstreuer, Pankaj R. Daga, Sean Ekins, Kamel Mansouri, Liguo Wang, Judy Strickland, Matthew J. Hirn, Sudin Bhattacharya, Dac-Trung Nguyen, Emilio Benfenati, Ignacio J. Tripodi, Amanda K. Parks, Garett Goh, Dennis G. Thomas, Glenn J. Myatt, Prachi Pradeep, Gergely Zahoranszky-Kohalmi, Anton Simeonov, Arthur C. Silva, Grace Patlewicz, Timothy Sheils, Stephen Boyd, Agnes L. Karmaus, Ahmed Sayed, Alex M. Clark, Todd M. Martin, Pavel Karpov, Jeffery M. Gearhart, Robert Rallo, D Allen, Charles Siegel, Zhen Zhang, Zijun Xiao, Alexander Tropsha, Stephen J. Capuzzi, Alexandru Korotcov, Carolina Horta Andrade, Noel Southall, Viviana Consonni, Igor V. Tetko, Jeremy M. Fitzpatrick, Andrew J. Wedlake, Denis Fourches, Zhongyu Wang, Vinicius M. Alves, Eugene N. Muratov, Timothy E. H. Allen, Andrea Mauri, James B. Brown, Alexandre Varnek, Yun Tang, Sanjeeva J. Wijeyesakere, Daniel P. Russo, Cosimo Toma, Christopher M. Grulke, Michael S. Lawless, Domenico Gadaleta, Paritosh Pande, Thomas Hartung, Jonathan M. Goodman, Kristijan Vukovic, Joyce V. Bastos, Daniela Trisciuzzi, Fagen F. Zhang, Domenico Alberga, Thomas Luechtefeld, Dan Marsh, Tyler R. Auernhammer, Shannon M. Bell, Xinhao Li, Brian J. Teppen, F. Lunghini, Sergey Sosnin, Hao Zhu, Feng Gao, Craig Rowlands, Tongan Zhao, R Todeschini, Valery Tkachenko, Francesca Grisoni, Hongbin Yang, Yaroslav Chushak, Maxim V. Fedorov, Heather L. Ciallella, Gilles Marcou, Goodman, Jonathan [0000-0002-8693-9136], Yang, Hongbin [0000-0001-6740-1632], Apollo - University of Cambridge Repository, Mansouri, K, Karmaus, A, Fitzpatrick, J, Patlewicz, G, Pradeep, P, Alberga, D, Alepee, N, Allen, T, Allen, D, Alves, V, Andrade, C, Auernhammer, T, Ballabio, D, Bell, S, Benfenati, E, Bhattacharya, S, Bastos, J, Boyd, S, Brown, J, Capuzzi, S, Chushak, Y, Ciallella, H, Clark, A, Consonni, V, Daga, P, Ekins, S, Farag, S, Fedorov, M, Fourches, D, Gadaleta, D, Gao, F, Gearhart, J, Goh, G, Goodman, J, Grisoni, F, Grulke, C, Hartung, T, Hirn, M, Karpov, P, Korotcov, A, Lavado, G, Lawless, M, Li, X, Luechtefeld, T, Lunghini, F, Mangiatordi, G, Marcou, G, Marsh, D, Martin, T, Mauri, A, Muratov, E, Myatt, G, Nguyen, D, Nicolotti, O, Note, R, Pande, P, Parks, A, Peryea, T, Polash, A, Rallo, R, Roncaglioni, A, Rowlands, C, Ruiz, P, Russo, D, Sayed, A, Sayre, R, Sheils, T, Siegel, C, Silva, A, Simeonov, A, Sosnin, S, Southall, N, Strickland, J, Tang, Y, Teppen, B, Tetko, I, Thomas, D, Tkachenko, V, Todeschini, R, Toma, C, Tripodi, I, Trisciuzzi, D, Tropsha, A, Varnek, A, Vukovic, K, Wang, Z, Wang, L, Waters, K, Wedlake, A, Wijeyesakere, S, Wilson, D, Xiao, Z, Yang, H, Zahoranszky-Kohalmi, G, Zakharov, A, Zhang, F, Zhang, Z, Zhao, T, Zhu, H, Zorn, K, Casey, W, Kleinstreuer, N, Chimie de la matière complexe (CMC), and Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Health, Toxicology and Mutagenesis ,010501 environmental sciences ,Bioinformatics ,01 natural sciences ,03 medical and health sciences ,0302 clinical medicine ,Government Agencies ,CHIM/01 - CHIMICA ANALITICA ,Toxicity Tests, Acute ,Medicine ,Animals ,Computer Simulation ,030212 general & internal medicine ,United States Environmental Protection Agency ,consensus analysi ,0105 earth and related environmental sciences ,QSAR ,business.industry ,Research ,Acute Toxicity ,Public Health, Environmental and Occupational Health ,Acute toxicity ,United States ,3. Good health ,Rats ,machine learning ,Systemic toxicity ,13. Climate action ,Erratum ,business ,[CHIM.CHEM]Chemical Sciences/Cheminformatics ,Potential toxicity - Abstract
BACKGROUND: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). METHODS: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495.
- Published
- 2021
37. Indole-core inhibitors of influenza a neuraminidase: iterative medicinal chemistry and molecular modeling.
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Tsedilin A, Schmidtke M, Monakhova N, Leneva I, Falynskova I, Khrenova M, Lane TR, Ekins S, and Makarov V
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- Animals, Dogs, Structure-Activity Relationship, Madin Darby Canine Kidney Cells, Molecular Structure, Models, Molecular, Influenza A virus drug effects, Influenza A virus enzymology, Dose-Response Relationship, Drug, Chemistry, Pharmaceutical, Humans, Mice, Microbial Sensitivity Tests, Virus Replication drug effects, Neuraminidase antagonists & inhibitors, Neuraminidase metabolism, Antiviral Agents pharmacology, Antiviral Agents chemistry, Antiviral Agents chemical synthesis, Indoles pharmacology, Indoles chemistry, Indoles chemical synthesis, Enzyme Inhibitors pharmacology, Enzyme Inhibitors chemistry, Enzyme Inhibitors chemical synthesis
- Abstract
Influenza viruses that cause seasonal and pandemic flu are a permanent health threat. The surface glycoprotein, neuraminidase, is crucial for the infectivity of the virus and therefore an attractive target for flu drug discovery campaigns. We have designed and synthesized more than 40 3-indolinone derivatives. We mainly investigated the role of substituents at the 2 position of the core as well as the introduction of substituents or a nitrogen atom in the fused phenyl ring of the core for inhibition of influenza virus neuraminidase activity and replication in vitro and in vivo. After evaluating the compounds for their ability to inhibit the viral neuraminidase, six potent inhibitors 3c, 3e, 7c, 12o, 12v, 18d were progressed to evaluate for cytotoxicity and inhibition of influenza virus A/PR/8/34 replication in in MDCK cells. Two hit compounds 3e and 12o were tested in an animal model of influenza virus infection. Molecular mechanism of the 3-indolinone derivatives interactions with the neuraminidase was revealed in molecular dynamic simulations. Proposed inhibitors bind to the 430-cavity that is different from the conventional binding site of commercial compounds. The most promising 3-indolinone inhibitors demonstrate stronger interactions with the neuraminidase in molecular models that supports proposed binding site., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)
- Published
- 2024
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38. Machine learning-aided search for ligands of P2Y 6 and other P2Y receptors.
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Puhl AC, Lewicki SA, Gao ZG, Pramanik A, Makarov V, Ekins S, and Jacobson KA
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- Humans, Ligands, Drug Discovery methods, Machine Learning, Receptors, Purinergic P2 metabolism, Receptors, Purinergic P2 drug effects
- Abstract
The P2Y
6 receptor, activated by uridine diphosphate (UDP), is a target for antagonists in inflammatory, neurodegenerative, and metabolic disorders, yet few potent and selective antagonists are known to date. This prompted us to use machine learning as a novel approach to aid ligand discovery, with pharmacological evaluation at three P2YR subtypes: initially P2Y6 and subsequently P2Y1 and P2Y14 . Relying on extensive published data for P2Y6 R agonists, we generated and validated an array of classification machine learning model using the algorithms deep learning (DL), adaboost classifier (ada), Bernoulli NB (bnb), k-nearest neighbors (kNN) classifier, logistic regression (lreg), random forest classifier (rf), support vector classification (SVC), and XGBoost (XGB) classifier models, and the common consensus was applied to molecular selection of 21 diverse structures. Compounds were screened using human P2Y6 R-induced functional calcium transients in transfected 1321N1 astrocytoma cells and fluorescent binding inhibition at closely related hP2Y14 R expressed in CHO cells. The hit compound ABBV-744, an experimental anticancer drug with a 6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine scaffold, had multifaceted interactions with the P2YR family: hP2Y6 R inhibition in a non-surmountable fashion, suggesting that noncompetitive antagonism, and hP2Y1 R enhancement, but not hP2Y14 R binding inhibition. Other machine learning-selected compounds were either weak (experimental anti-asthmatic drug AZD5423 with a phenyl-1H-indazole scaffold) or inactive in inhibiting the hP2Y6 R. Experimental drugs TAK-593 and GSK1070916 (100 µM) inhibited P2Y14 R fluorescent binding by 50% and 38%, respectively, and all other compounds by < 20%. Thus, machine learning has led the way toward revealing previously unknown modulators of several P2YR subtypes that have varied effects., Competing Interests: Declarations Ethics approval Ethics approval is not applicable. This study does not involve any human or animal studies. Competing interests SE owner and ACP employee of Collaborations Pharmaceuticals, Inc. Inclusion and diversity We support inclusive, diverse, and equitable conduct of research., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)- Published
- 2024
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39. Predicting the Hallucinogenic Potential of Molecules Using Artificial Intelligence.
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Urbina F, Jones T, Harris JS, Snyder SH, Lane TR, and Ekins S
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- Humans, Animals, Machine Learning, Lysergic Acid Diethylamide pharmacology, Support Vector Machine, Mice, Hallucinogens pharmacology, Artificial Intelligence
- Abstract
The development of new drugs addressing serious mental health and other disorders should avoid the psychedelic experience. Analogs of psychedelic drugs can have clinical utility and are termed "psychoplastogens". These represent promising candidates for treating opioid use disorder to reduce drug dependence, with rarely reported serious adverse effects. This drug abuse cessation is linked to the induction of neuritogenesis and increased neuroplasticity, a hallmark of psychedelic molecules, such as lysergic acid diethylamine. Some, but not all psychoplastogens may act through the G-protein coupled receptor (GPCR) 5HT
2A whereas others may display very different polypharmacology making prediction of hallucinogenic potential challenging. In the process of developing tools to help design new psychoplastogens, we have used artificial intelligence in the form of machine learning classification models for predicting psychedelic effects using a published in vitro data set from PsychLight (support vector classification (SVC), area under the curve (AUC) 0.74) and in vivo human data derived from books from Shulgin and Shulgin (SVC, AUC, 0.72) with nested five-fold cross validation. We have also explored conformal predictors with ECFP6 and electrostatic descriptors in an effort to optimize them. These models have been used to predict known 5HT2A agonists to assess their potential to act as psychedelics and induce hallucinations for PsychLight (SVC, AUC 0.97) and Shulgin and Shulgin (random forest, AUC 0.71). We have tested these models with head twitch data from the mouse. This predictive capability is desirable to reliably design new psychoplastogens that lack in vivo hallucinogenic potential and help assess existing and future molecules for this potential. These efforts also provide useful insights into understanding the psychedelic structure activity relationship.- Published
- 2024
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40. Oral Pyronaridine Tetraphosphate Reduces Tissue Presence of Parasites in a Mouse Model of Chagas Disease.
- Author
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Siqueira-Neto JL, Lane TR, Bernatchez JA, Calvet Alvarez CM, Barbosa da Silva E, Giardini MA, and Ekins S
- Abstract
The eukaryotic parasite Trypanosoma cruzi ( T. cruzi ) is responsible for Chagas disease, which results in heart failure in patients. The disease is more common in Latin America, and is an emerging infection with The Centers for Disease Control estimating that greater than 300,000 people are currently infected in the United States. This disease has also spread from South and Central America, where it is endemic to many other countries, including Australia, Japan, and Spain. Current therapy for Chagas disease is inadequate due to limited efficacy in the indeterminate and chronic phases of the disease, in addition to the adverse effects from nifurtimox and benznidazole, which are nitro-containing drugs used for therapy. There is a clear need for new therapies for the Chagas disease. Using a computational machine learning approach, we have previously shown that the antimalarial pyronaridine tetraphosphate is active against T. cruzi Brazil-luc in vitro against parasites infecting a myoblast cell line and is also active in vivo in an acute mouse model of Chagas disease when dosed i.p. We now further evaluated oral pyronaridine as a monotherapy to determine the minimum effective dose to treat acute and chronic models of Chagas disease. Our results for T. cruzi Brazil-luc demonstrated daily oral dosing with pyronaridine from 150 to 600 mg/kg resulted in statistically significant inhibition in the 7 day acute mouse model. Combination therapy with daily dosing of benznidazole and pyronaridine in the acute infection model demonstrated that 300 mg/kg pyronaridine could return statistically significant antiparasitic activity to a subtherapetic 10 mg/kg benznidazole. In contrast, pyronaridine as monotherapy or combined with benznidazole lacked efficacy in the chronic mouse model, whereas 100 mg/kg benznidazole alone demonstrated undetectable parasites in the heart of mice. Pyronaridine requires further assessment in other chronic models to identify if it can be used beyond the acute stage of T. cruzi infection., Competing Interests: The authors declare the following competing financial interest(s): S.E. is owner of Collaborations Pharmaceuticals Inc., and T.R.L. is an employee at Collaborations Pharmaceuticals Inc. All other authors are associates of the University of California, San Diego., (© 2024 The Authors. Published by American Chemical Society.)
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- 2024
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41. Near-Term Quantum Classification Algorithms Applied to Antimalarial Drug Discovery.
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Dorsey MA, Dsouza K, Ranganath D, Harris JS, Lane TR, Urbina F, and Ekins S
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- Algorithms, Quantitative Structure-Activity Relationship, Antimalarials chemistry, Antimalarials pharmacology, Drug Discovery methods, Machine Learning, Quantum Theory
- Abstract
Computational approaches are widely applied in drug discovery to explore properties related to bioactivity, physiochemistry, and toxicology. Over at least the last 20 years, the exploitation of machine learning on molecular data sets has been used to understand the structure-activity relationships that exist between biomolecules and druggable targets. More recently, these methods have also seen application for phenotypic screening data for neglected diseases such as tuberculosis and malaria. Herein, we apply machine learning to build quantum Quantitative Structure Activity Relationship models from antimalarial data sets. There is a continual need for new antimalarials to address drug resistance, and the readily available in vitro data sets could be utilized with newer machine learning approaches as these develop. Furthermore, quantum machine learning is a relatively new method that uses a quantum computer to perform the calculations. First, we present a classical-quantum hybrid computational approach by building a Latent Bernoulli Autoencoder machine learning model for compressing bit-vector descriptors to a size that can be adapted to quantum computers for classification tasks with limited loss of embedded information. Second, we apply our method for feature map compression to quantum classification algorithms, including a completely novel machine learning algorithm with no analogy in classical computers: the Quantum Fourier Transform Classifier. We apply both these approaches to build quantum machine learning models for small-molecule antimalarials with quantum simulation software and then benchmark these quantum models against classical machine learning approaches. While there are many challenges currently facing the development of reliable quantum computers, our results demonstrate that there is potential for the use of this technology in the field of drug discovery.
- Published
- 2024
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42. In silico ADME/tox comes of age: twenty years later.
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Ekins S, Lane TR, Urbina F, and Puhl AC
- Subjects
- Humans, Drug Discovery, Pharmaceutical Preparations metabolism, Models, Biological, Pharmacokinetics, Drug-Related Side Effects and Adverse Reactions, Computer Simulation
- Abstract
In the early 2000s pharmaceutical drug discovery was beginning to use computational approaches for absorption, distribution, metabolism, excretion and toxicity (ADME/Tox, also known as ADMET) prediction. This emphasis on prediction was an effort to reduce the risk of later stage failures from ADME/Tox.Much has been written in the intervening twenty plus years and significant expenditure has occurred in companies developing these in silico capabilities which can be gleaned from publications. It is therefore an appropriate time to briefly reflect on what was proposed then and what the reality is today.20 years ago, we tended to optimise bioactivity and perhaps one ADME/Tox property at a time. Previously pharmaceutical companies needed a whole infrastructure for models - in silico and in vitro experts, IT, champions on a project team, educators and management support. Now we are in the age of generative de novo design where bioactivity and many ADME/Tox properties can be optimised and large language model technologies are available.There are also some challenges such as the focus on very large molecules which may be outside of current ADME/Tox models.We provide an opportunity to look forward with the increasing public data for ADME/Tox as well as expanded types of algorithms available.
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- 2024
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43. The Goldilocks paradigm: comparing classical machine learning, large language models, and few-shot learning for drug discovery applications.
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Snyder SH, Vignaux PA, Ozalp MK, Gerlach J, Puhl AC, Lane TR, Corbett J, Urbina F, and Ekins S
- Abstract
Recent advances in machine learning (ML) have led to newer model architectures including transformers (large language models, LLMs) showing state of the art results in text generation and image analysis as well as few-shot learning (FSLC) models which offer predictive power with extremely small datasets. These new architectures may offer promise, yet the 'no-free lunch' theorem suggests that no single model algorithm can outperform at all possible tasks. Here, we explore the capabilities of classical (SVR), FSLC, and transformer models (MolBART) over a range of dataset tasks and show a 'goldilocks zone' for each model type, in which dataset size and feature distribution (i.e. dataset "diversity") determines the optimal algorithm strategy. When datasets are small ( < 50 molecules), FSLC tend to outperform both classical ML and transformers. When datasets are small-to-medium sized (50-240 molecules) and diverse, transformers outperform both classical models and few-shot learning. Finally, when datasets are of larger and of sufficient size, classical models then perform the best, suggesting that the optimal model to choose likely depends on the dataset available, its size and diversity. These findings may help to answer the perennial question of which ML algorithm is to be used when faced with a new dataset., (© 2024. The Author(s).)
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- 2024
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44. In Vitro Characterization and Rescue of VX Metabolism in Human Liver Microsomes.
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Lane TR, Koebel D, Lucas E, Moyer R, and Ekins S
- Subjects
- Humans, Edetic Acid pharmacology, Edetic Acid metabolism, Cytochrome P-450 Enzyme System metabolism, Microsomes, Liver metabolism, Organothiophosphorus Compounds metabolism, Cholinesterase Inhibitors metabolism, Cholinesterase Inhibitors pharmacology
- Abstract
Venomous agent X (VX) is an organophosphate acetylcholinesterase (AChE) inhibitor, and although it is one of the most toxic AChE inhibitors known, the extent of metabolism in humans is not currently well understood. The known metabolism in humans is limited to the metabolite identification from a single victim of the Osaka poisoning in 1994, which allowed for the identification of several metabolic products. VX has been reported to be metabolized in vitro by paraoxonase-1 and phosphotriesterase, although their binding constants are many orders of magnitude above the LD
50 , suggesting limited physiologic relevance. Using incubation with human liver microsomes (HLMs), we have now characterized the metabolism of VX and the formation of multiple metabolites as well as identified a Food and Drug Administration-approved drug [ethylenediaminetetraacetic acid (EDTA)] that enhances the metabolic rate. HLM incubation alone shows a pronounced increase in the metabolism of VX compared with buffer, suggesting that cytochrome P450-mediated metabolism of VX is occurring. We identified a biphasic decay with two distinct rates of metabolism. The enhancement of VX metabolism in multiple buffers was assessed to attempt to mitigate the effect of hydrolysis rates. The formation of VX metabolites was shown to be shifted with HLMs, suggesting a pathway enhancement over simple hydrolysis. Additionally, our investigation of hydrolysis rates in various common buffers used in biologic assays discovered dramatic differences in VX stability. The new human in vitro VX metabolic data reported points to a potential in vivo treatment strategy (EDTA) for rescue in individuals that are poisoned though enhancement of metabolism alongside existing treatments. SIGNIFICANCE STATEMENT: Venomous agent X (VX) is a potent acetylcholinesterase inhibitor and chemical weapon. To date, we do not possess a clear understanding of its metabolism in humans that would assist us in treating those exposed to it. This study now describes the human liver microsomal metabolism of VX and identifies ethylenediaminetetraacetic acid, which appears to enhance the rate of metabolism. This may provide a potential treatment option for human VX poisoning., (Copyright © 2024 by The American Society for Pharmacology and Experimental Therapeutics.)- Published
- 2024
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45. Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus.
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Yang JJ, Goff A, Wild DJ, Ding Y, Annis A, Kerber R, Foote B, Passi A, Duerksen JL, London S, Puhl AC, Lane TR, Braunstein M, Waddell SJ, and Ekins S
- Subjects
- Humans, Niclosamide pharmacology, Drug Repositioning, Nontuberculous Mycobacteria genetics, Mycobacterium tuberculosis genetics, Mycobacterium abscessus, Mycobacterium Infections, Nontuberculous microbiology, Tuberculosis drug therapy, Tuberculosis microbiology, Salicylanilides
- Abstract
Tuberculosis (TB) is still a major global health challenge, killing over 1.5 million people each year, and hence, there is a need to identify and develop novel treatments for Mycobacterium tuberculosis (M. tuberculosis). The prevalence of infections caused by nontuberculous mycobacteria (NTM) is also increasing and has overtaken TB cases in the United States and much of the developed world. Mycobacterium abscessus (M. abscessus) is one of the most frequently encountered NTM and is difficult to treat. We describe the use of drug-disease association using a semantic knowledge graph approach combined with machine learning models that has enabled the identification of several molecules for testing anti-mycobacterial activity. We established that niclosamide (M. tuberculosis IC
90 2.95 μM; M. abscessus IC90 59.1 μM) and tribromsalan (M. tuberculosis IC90 76.92 μM; M. abscessus IC90 147.4 μM) inhibit M. tuberculosis and M. abscessus in vitro. To investigate the mode of action, we determined the transcriptional response of M. tuberculosis and M. abscessus to both compounds in axenic log phase, demonstrating a broad effect on gene expression that differed from known M. tuberculosis inhibitors. Both compounds elicited transcriptional responses indicative of respiratory pathway stress and the dysregulation of fatty acid metabolism., Competing Interests: Declaration of competing interest S.E. is owner, and A.C.P. and T.R.L. are employees of Collaborations Pharmaceuticals, Inc. J.J.Y., D.J.W., Y.D., B.F., and J.L.D., are employees, and D.J.W., B.F., R.K., and S.L., are board members, of Data2Discovery, Inc., which has applied for patent protections covering discoveries described herein. All others have no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)- Published
- 2024
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46. Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors.
- Author
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Ozalp MK, Vignaux PA, Puhl AC, Lane TR, Urbina F, and Ekins S
- Subjects
- Humans, Models, Molecular, Acetylcholinesterase metabolism, Acetylcholinesterase chemistry, Alzheimer Disease drug therapy, Butyrylcholinesterase metabolism, Butyrylcholinesterase chemistry, Cholinesterase Inhibitors pharmacology, Cholinesterase Inhibitors chemistry, Deep Learning
- Abstract
Butyrylcholinesterase (BChE) is a target of interest in late-stage Alzheimer's Disease (AD) where selective BChE inhibitors (BIs) may offer symptomatic treatment without the harsh side effects of acetylcholinesterase (AChE) inhibitors. In this study, we explore multiple machine learning strategies to identify BIs in silico , optimizing for precision over all other metrics. We compare state-of-the-art supervised contrastive learning (CL) with deep learning (DL) and Random Forest (RF) machine learning, across single and sequential modeling configurations, to identify the best models for BChE selectivity. We used these models to virtually screen a vendor library of 5 million compounds for BIs and tested 20 of these compounds in vitro . Seven of the 20 compounds displayed selectivity for BChE over AChE, reflecting a hit rate of 35% for our model predictions, suggesting a highly efficient strategy for modeling selective inhibition.
- Published
- 2024
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47. Identification of New Modulators and Inhibitors of Palmitoyl-Protein Thioesterase 1 for CLN1 Batten Disease and Cancer.
- Author
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Puhl AC, Raman R, Havener TM, Minerali E, Hickey AJ, and Ekins S
- Abstract
Palmitoyl-protein thioesterase 1 (PPT1) is an understudied enzyme that is gaining attention due to its role in the depalmitoylation of several proteins involved in neurodegenerative diseases and cancer. PPT1 is overexpressed in several cancers, specifically cholangiocarcinoma and esophageal cancers. Inhibitors of PPT1 lead to cell death and have been shown to enhance the killing of tumor cells alongside known chemotherapeutics. PPT1 is hence a viable target for anticancer drug development. Furthermore, mutations in PPT1 cause a lysosomal storage disorder called infantile neuronal ceroid lipofuscinosis (CLN1 disease). Molecules that can inhibit, stabilize, or modulate the activity of this target are needed to address these diseases. We used PPT1 enzymatic assays to identify molecules that were subsequently tested by using differential scanning fluorimetry and microscale thermophoresis. Selected compounds were also tested in neuroblastoma cell lines. The resulting PPT1 screening data was used for building machine learning models to help select additional compounds for testing. We discovered two of the most potent PPT1 inhibitors reported to date, orlistat (IC
50 178.8 nM) and palmostatin B (IC50 11.8 nM). When tested in HepG2 cells, it was found that these molecules had decreased activity, indicating that they were likely not penetrating the cells. The combination of in vitro enzymatic and biophysical assays enabled the identification of several molecules that can bind or inhibit PPT1 and may aid in the discovery of modulators or chaperones. The molecules identified could be used as a starting point for further optimization as treatments for other potential therapeutic applications outside CLN1 disease, such as cancer and neurological diseases., Competing Interests: The authors declare the following competing financial interest(s): S.E. is the owner and A.C.P., R.R., and E.M. are employees of Collaborations Pharmaceuticals, Inc., (© 2024 The Authors. Published by American Chemical Society.)- Published
- 2024
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48. High-Throughput Phenotypic Screening and Machine Learning Methods Enabled the Selection of Broad-Spectrum Low-Toxicity Antitrypanosomatidic Agents.
- Author
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Linciano P, Quotadamo A, Luciani R, Santucci M, Zorn KM, Foil DH, Lane TR, Cordeiro da Silva A, Santarem N, B Moraes C, Freitas-Junior L, Wittig U, Mueller W, Tonelli M, Ferrari S, Venturelli A, Gul S, Kuzikov M, Ellinger B, Reinshagen J, Ekins S, and Costi MP
- Subjects
- High-Throughput Screening Assays, Antiparasitic Agents, Trypanosoma cruzi, Trypanosoma brucei brucei, Leishmania infantum
- Abstract
Broad-spectrum anti-infective chemotherapy agents with activity against Trypanosomes , Leishmania, and Mycobacterium tuberculosis species were identified from a high-throughput phenotypic screening program of the 456 compounds belonging to the Ty-Box, an in-house industry database. Compound characterization using machine learning approaches enabled the identification and synthesis of 44 compounds with broad-spectrum antiparasitic activity and minimal toxicity against Trypanosoma brucei , Leishmania Infantum, and Trypanosoma cruzi . In vitro studies confirmed the predictive models identified in compound 40 which emerged as a new lead, featured by an innovative N -(5-pyrimidinyl)benzenesulfonamide scaffold and promising low micromolar activity against two parasites and low toxicity. Given the volume and complexity of data generated by the diverse high-throughput screening assays performed on the compounds of the Ty-Box library, the chemoinformatic and machine learning tools enabled the selection of compounds eligible for further evaluation of their biological and toxicological activities and aided in the decision-making process toward the design and optimization of the identified lead.
- Published
- 2023
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49. 1-Sulfonyl-3-amino-1 H -1,2,4-triazoles as Yellow Fever Virus Inhibitors: Synthesis and Structure-Activity Relationship.
- Author
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Kazakova E, Lane TR, Jones T, Puhl AC, Riabova O, Makarov V, and Ekins S
- Abstract
Yellow fever virus (YFV) transmitted by infected mosquitoes causes an acute viral disease for which there are no approved small-molecule therapeutics. Our recently developed machine learning models for YFV inhibitors led to the selection of a new pyrazolesulfonamide derivative RCB16003 with acceptable in vitro activity. We report that the N -phenyl-1-(phenylsulfonyl)-1 H -1,2,4-triazol-3-amine class, which was recently identified as active non-nucleoside reverse transcriptase inhibitors against HIV-1, can also be repositioned as inhibitors of yellow fever virus replication. As compared to other Flaviviridae or Togaviridae family viruses tested, both compounds RCB16003 and RCB16007 demonstrate selectivity for YFV over related viruses, with only RCB16007 showing some inhibition of the West Nile virus (EC
50 7.9 μM, CC50 17 μM, SI 2.2). We also describe the absorption, distribution, metabolism, and excretion (ADME) in vitro and pharmacokinetics (PK) for RCB16007 in mice. This compound had previously been shown to not inhibit hERG, and we now describe that it has good metabolic stability in mouse and human liver microsomes, low levels of CYP inhibition, high protein binding, and no indication of efflux in Caco-2 cells. A single-dose oral PK study in mice has a T1/2 of 3.4 h and Cmax of 1190 ng/mL, suggesting good availability and stability. We now propose that the N -phenyl-1-(phenylsulfonyl)-1 H -1,2,4-triazol-3-amine class may be prioritized for in vivo efficacy testing against YFV., Competing Interests: The authors declare the following competing financial interest(s): S.E. is owner, A.C.P, T.J. and T.R.L. are employees of Collaborations Pharmaceuticals, Inc. Others have no competing interests. A provisional patent on this work has been submitted., (© 2023 The Authors. Published by American Chemical Society.)- Published
- 2023
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50. Synthesis and Evaluation of 9-Aminoacridines with SARS-CoV-2 Antiviral Activity.
- Author
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Jones T, Monakhova N, Guivel-Benhassine F, Lepioshkin A, Bruel T, Lane TR, Schwartz O, Puhl AC, Makarov V, and Ekins S
- Abstract
There have been relatively few small molecules developed with direct activity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Two existing antimalarial drugs, pyronaridine and quinacrine, display whole cell activity against SARS-CoV-2 in A549 + ACE2 cells (pretreatment, IC
50 = 0.23 and 0.19 μM, respectively) with moderate cytotoxicity (CC50 = 11.53 and 9.24 μM, respectively). Moreover, pyronaridine displays in vitro activity against SARS-CoV-2 PLpro (IC50 = 1.8 μM). Given their existing antiviral activity, these compounds are strong candidates for repurposing against COVID-19 and prompt us to study the structure-activity relationship of the 9-aminoacridine scaffold against SARS-CoV-2 using traditional medicinal chemistry to identify promising new analogs. Our studies identified several novel analogs possessing potent in vitro activity in U2-OS ACE2 GFP 1-10 and 1-11 (IC50 < 1.0 μM) as well as moderate cytotoxicity (CC50 > 4.0 μM). Compounds such as 7g , 9c , and 7e were more active, demonstrating selectivity indices SI > 10, and 9c displayed the strongest activity (IC50 ≤ 0.42 μM, CC50 ≥ 4.41 μM, SI > 10) among them, indicating that it has potential as a new lead molecule in this series against COVID-19., Competing Interests: The authors declare the following competing financial interest(s): SE is CEO of Collaborations Pharmaceuticals, Inc. TJ, TRL and ACP are employees at Collaborations Pharmaceuticals, Inc. Collaborations Pharmaceuticals, Inc. has obtained FDA orphan drug designations for pyronaridine, tilorone and quinacrine for use against Ebola. CPI has also filed a provisional patent for use of these molecules against Marburg and other viruses. The other authors declare that they have no conflict of interest., (© 2023 The Authors. Published by American Chemical Society.)- Published
- 2023
- Full Text
- View/download PDF
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