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Manjunatha UH, Lakshminarayana SB, Jumani RS, Chao AT, Young JM, Gable JE, Knapp M, Hanna I, Galarneau JR, Cantwell J, Kulkarni U, Turner M, Lu P, Darrell KH, Watson LC, Chan K, Patra D, Mamo M, Luu C, Cuellar C, Shaul J, Xiao L, Chen YB, Carney SK, Lakshman J, Osborne CS, Zambriski JA, Aziz N, Sarko C, Diagana TT. Cryptosporidium PI(4)K inhibitor EDI048 is a gut-restricted parasiticidal agent to treat paediatric enteric cryptosporidiosis. Nat Microbiol 2024:10.1038/s41564-024-01810-x. [PMID: 39379634 DOI: 10.1038/s41564-024-01810-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 08/15/2024] [Indexed: 10/10/2024]
Abstract
Diarrhoeal disease caused by Cryptosporidium is a major cause of morbidity and mortality in young and malnourished children from low- and middle-income countries, with no vaccine or effective treatment. Here we describe the discovery of EDI048, a Cryptosporidium PI(4)K inhibitor, designed to be active at the infection site in the gastrointestinal tract and undergo rapid metabolism in the liver. By using mutational analysis and crystal structure, we show that EDI048 binds to highly conserved amino acid residues in the ATP-binding site. EDI048 is orally efficacious in an immunocompromised mouse model despite negligible circulating concentrations, thus demonstrating that gastrointestinal exposure is necessary and sufficient for efficacy. In neonatal calves, a clinical model of cryptosporidiosis, EDI048 treatment resulted in rapid resolution of diarrhoea and significant reduction in faecal oocyst shedding. Safety and pharmacological studies demonstrated predictable metabolism and low systemic exposure of EDI048, providing a substantial safety margin required for a paediatric indication. EDI048 is a promising clinical candidate for the treatment of life-threatening paediatric cryptosporidiosis.
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Affiliation(s)
| | | | - Rajiv S Jumani
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | - Alexander T Chao
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | | | - Jonathan E Gable
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | - Mark Knapp
- Biomedical Research, Novartis, Emeryville, CA, USA
| | - Imad Hanna
- Biomedical Research, Novartis, East Hanover, NJ, USA
| | | | | | | | | | - Peichao Lu
- Biomedical Research, Novartis, Emeryville, CA, USA
| | - Kristen H Darrell
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
- Metagenomi, Inc., Emeryville, CA, USA
| | - Lucy C Watson
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | - Katherine Chan
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | - Debjani Patra
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | | | | | | | - Jacob Shaul
- Biomedical Research, Novartis, Emeryville, CA, USA
- Absci Corporation, Vancouver, WA, USA
| | - Linda Xiao
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | - Ying-Bo Chen
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | - Shannon K Carney
- Department of Population Health Sciences, College of Veterinary Medicine, Center for One Health Research, Blacksburg, VA, USA
- Cornell University, College of Veterinary Medicine, Department of Population Medicine and Diagnostic Sciences, Ithaca, NY, USA
| | - Jay Lakshman
- Novartis Pharmaceutical Corporation, East Hanover, NJ, USA
| | - Colin S Osborne
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
| | - Jennifer A Zambriski
- Department of Population Health Sciences, College of Veterinary Medicine, Center for One Health Research, Blacksburg, VA, USA
- Veterinarians for Global Solutions, Washington, DC, USA
| | - Natasha Aziz
- Global Health, Biomedical Research, Novartis, Emeryville, CA, USA
- Genentech Research and Early Development, South San Francisco, CA, USA
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2
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Bak SM, Back SM, Kim DY, Jung S, Jeung NY, Kim NY, Han KH, Kim YB, Lee BS, Park JH, Cho HJ, Lee HG, Ozden O, Kim SK, Park SH. Differential genotoxicity of Polygoni Multiflori in rat and human: insights from Ames test and S9 metabolic activation system. Sci Rep 2024; 14:21433. [PMID: 39271730 PMCID: PMC11399298 DOI: 10.1038/s41598-024-72283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
The Ames test is used worldwide to initially screen the mutagenic potential of new chemicals. In the standard Ames test, S. typhimurium strains (TA100, TA98, TA1535, and TA1537) and Escherichia coli (WP2uvrA) are treated with substances with/without cytochrome P450s (CYPs)-induced rat S9 fractions for identifying mutagens and pro-mutagens. However, many substances show completely different toxicity patterns depending on whether the liver S9 fraction belongs to rats or humans. The natural product Polygoni Multiflori Radix (PMR) can also show bacterial reverse mutation, followed by the rat or human liver S9 fraction. While PMR elicits reverse mutations in the TA1537 strain in rat liver S9 but not in human liver S9, this mechanism has not been verified yet. To explain this, the differences in metabolic enzymes compositions commonly observed between rats and humans have been implicated. This study aimed to explore the key factors that cause differences in the genotoxicity of PMR between rat and human liver S9 metabolic enzymes. The results of next-generation sequencing (NGS) analysis showed that both rat and human metabolic enzymes caused similar mutations in TA1537. However, when the metabolic enzymes in each S9 fraction were analyzed using ion mobility tandem mass spectrometry (IM-MS), rat- and human-specific enzymes were identified among the cytochrome (CYP) family, especially aryl hydrocarbon receptor (AHR)-related CYPs. These findings suggest that CYP1A1 isoforms contribute to the mechanism of PMR in the Ames test. Therefore, an in vitro Ames test might be more reliable in predicting genotoxicity for both rodents and humans. This will also help overcome the limitations of laboratory animal-based toxicity evaluations, which provide unreliable results due to interspecies differences between humans and rodents.
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Affiliation(s)
- Su-Min Bak
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Seng-Min Back
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
- College of Pharmacy, Chungnam National University, 9 Daehak-Ro, Yuseong-Gu, Daejeon, 34134, Republic of Korea
| | - Da Yeon Kim
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Soyoung Jung
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Na-Young Jeung
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Nan-Young Kim
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Kang-Hyun Han
- Regulatory Toxicology Research Division, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Yong-Bum Kim
- Department of Advanced Toxicology Research, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Byoung-Seok Lee
- Department of Advanced Toxicology Research, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Jun Hong Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju-Si, 58245, South Korea
| | - Hee Jun Cho
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hee Gu Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Ozkan Ozden
- Department of Bioengineering, Faculty of Engineering and Architecture, Kafkas University, 36100, Kars, Turkey
| | - Sang Kyum Kim
- College of Pharmacy, Chungnam National University, 9 Daehak-Ro, Yuseong-Gu, Daejeon, 34134, Republic of Korea.
| | - Seong-Hoon Park
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
- Toxicology Mechanism Research Division, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
- Genetic Toxicology Research Group, Toxicology Mechanism Research Division, Korea Institute of Toxicology, 141 Gajeong-Ro, Yuseong-Gu, Daejeon, 34114, Republic of Korea.
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3
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Niu Z, Xiao X, Wu W, Cai Q, Jiang Y, Jin W, Wang M, Yang G, Kong L, Jin X, Yang G, Chen H. PharmaBench: Enhancing ADMET benchmarks with large language models. Sci Data 2024; 11:985. [PMID: 39256394 PMCID: PMC11387650 DOI: 10.1038/s41597-024-03793-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024] Open
Abstract
Accurately predicting ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties early in drug development is essential for selecting compounds with optimal pharmacokinetics and minimal toxicity. Existing ADMET-related benchmark sets are limited in utility due to their small dataset sizes and the lack of representation of compounds used in drug discovery projects. These shortcomings hinder their application in model building for drug discovery. To address this issue, we propose a multi-agent data mining system based on Large Language Models that effectively identifies experimental conditions within 14,401 bioassays. This approach facilitates merging entries from different sources, culminating in the creation of PharmaBench. Additionally, we have developed a data processing workflow to integrate data from various sources, resulting in 156,618 raw entries. Through this workflow, we constructed PharmaBench, a comprehensive benchmark set for ADMET properties, which comprises eleven ADMET datasets and 52,482 entries. This benchmark set is designed to serve as an open-source dataset for the development of AI models relevant to drug discovery projects.
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Affiliation(s)
- Zhangming Niu
- MindRank AI, Hangzhou, Zhejiang, China
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Xianglu Xiao
- MindRank AI, Hangzhou, Zhejiang, China
- Bioengineering Department and Imperial-X, Imperial College London, London, W12 7SL, UK
| | - Wenfan Wu
- MindRank AI, Hangzhou, Zhejiang, China
- Department of Bioinformatics and Systems Biology, Huazhong University of Science and Technology College of Life Sciences and Technology, Wuhan, Hubei, China
- Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Qiwei Cai
- MindRank AI, Hangzhou, Zhejiang, China
| | | | | | | | | | | | - Xurui Jin
- MindRank AI, Hangzhou, Zhejiang, China
| | - Guang Yang
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK.
- Bioengineering Department and Imperial-X, Imperial College London, London, W12 7SL, UK.
- Cardiovascular Research Centre, Royal Brompton Hospital, London, SW3 6NP, UK.
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK.
| | - Hongming Chen
- Department of Bioinformatics and Systems Biology, Huazhong University of Science and Technology College of Life Sciences and Technology, Wuhan, Hubei, China.
- Guangzhou National Laboratory, Guangzhou, 510005, China.
- School of pharmaceutical sciences, Guangzhou Medical University, Guangzhou, 511495, China.
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4
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Novoyatlova US, Kudryavtseva AA, Bazhenov SV, Utkina AA, Fomin VV, Nevmyanov SA, Zhoshibekova BS, Fedyaeva MA, Kolobov MY, Manukhov IV. The Assessment of Methyl Methanesulfonate Absorption by Amphipods from the Environment Using Lux-Biosensors. BIOSENSORS 2024; 14:427. [PMID: 39329802 PMCID: PMC11430740 DOI: 10.3390/bios14090427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/18/2024] [Accepted: 08/29/2024] [Indexed: 09/28/2024]
Abstract
The ability of aquatic mesofauna representatives involved in trophic chains to sorb and accumulate toxicants is important for understanding the functioning of aquatic ecosystems and for fishing industry. This study investigated the capacity of marine amphipod Gammarus oceanicus and freshwater amphipods Eulimnogammarus vittatus and Gammarus lacustris to absorb the DNA-alkylating agent methyl methanesulfonate (MMS). The presence of alkylating agents in the environment and in the tissues of the amphipods was determined using whole-cell lux-biosensor Escherichia coli MG1655 pAlkA-lux, in which the luxCDABE genes from Photorhabdus luminescens, enabling the luminescence of the cell culture, are controlled by the PalkA promoter of DNA glycosylase. It was shown that within one day of incubation in water containing MMS at a concentration above 10 μM, the amphipods absorbed the toxicant and their tissues produce more alkylation damage to biosensor cells than the surrounding water. Concentrations of MMS above 1 mM in the environment caused the death of the amphipods before the toxicant could be significantly concentrated in their tissues. The sensitivity and the capacity to absorb MMS were found to be approximately the same for the marine amphipod G. oceanicus and the freshwater amphipods E. vittatus and G. lacustris.
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Affiliation(s)
- Uliana S Novoyatlova
- Moscow Center for Advanced Studies, Moscow 123592, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the RAS, Moscow 119071, Russia
| | | | | | - Anna A Utkina
- Moscow Center for Advanced Studies, Moscow 123592, Russia
| | - Vadim V Fomin
- Moscow Center for Advanced Studies, Moscow 123592, Russia
| | | | - Bagila S Zhoshibekova
- Department of Biology, Kazakh National Women's Teacher Training University, Almaty 050000, Kazakhstan
| | - Maria A Fedyaeva
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail Y Kolobov
- A.N. Severtsov Institute of Ecology and Evolution of the RAS, Moscow 119071, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Ilya V Manukhov
- Moscow Center for Advanced Studies, Moscow 123592, Russia
- Laboratory of Microbiology, BIOTECH University, Moscow 125080, Russia
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5
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Xu H, Zhao Y, Zhang Y, Han J, Zan P, He S, Bo X. Deep active learning with high structural discriminability for molecular mutagenicity prediction. Commun Biol 2024; 7:1071. [PMID: 39217273 PMCID: PMC11366013 DOI: 10.1038/s42003-024-06758-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
The assessment of mutagenicity is essential in drug discovery, as it may lead to cancer and germ cells damage. Although in silico methods have been proposed for mutagenicity prediction, their performance is hindered by the scarcity of labeled molecules. However, experimental mutagenicity testing can be time-consuming and costly. One solution to reduce the annotation cost is active learning, where the algorithm actively selects the most valuable molecules from a vast chemical space and presents them to the oracle (e.g., a human expert) for annotation, thereby rapidly improving the model's predictive performance with a smaller annotation cost. In this paper, we propose muTOX-AL, a deep active learning framework, which can actively explore the chemical space and identify the most valuable molecules, resulting in competitive performance with a small number of labeled samples. The experimental results show that, compared to the random sampling strategy, muTOX-AL can reduce the number of training molecules by about 57%. Additionally, muTOX-AL exhibits outstanding molecular structural discriminability, allowing it to pick molecules with high structural similarity but opposite properties.
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Affiliation(s)
- Huiyan Xu
- Shanghai Key Laboratory of Power Station Automation Technology, School of Mechatronics Engineering and Automation, Shanghai University, Shanghai, China
- Academy of Military Medical Sciences, Beijing, China
| | - Yanpeng Zhao
- Academy of Military Medical Sciences, Beijing, China
| | - Yixin Zhang
- Academy of Military Medical Sciences, Beijing, China
| | - Junshan Han
- Academy of Military Medical Sciences, Beijing, China
| | - Peng Zan
- Shanghai Key Laboratory of Power Station Automation Technology, School of Mechatronics Engineering and Automation, Shanghai University, Shanghai, China.
| | - Song He
- Academy of Military Medical Sciences, Beijing, China.
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing, China.
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Bertoli RM, Chung YJ, Difilippantonio MJ, Wokasch A, Marasco MR, Klimaszewski H, Gammell S, Zhu YJ, Walker RL, Cao D, Khanna A, Walter MJ, Doroshow JH, Meltzer PS, Aplan PD. The DNA Methyltransferase Inhibitor 5-Aza-4'-thio-2'-Deoxycytidine Induces C>G Transversions and Acute Lymphoid Leukemia Development. Cancer Res 2024; 84:2518-2532. [PMID: 38832931 PMCID: PMC11293964 DOI: 10.1158/0008-5472.can-23-2785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
DNA methyltransferase inhibitors (DNMTi), most commonly cytidine analogs, are compounds that decrease 5'-cytosine methylation. DNMTi are used clinically based on the hypothesis that cytosine demethylation will lead to re-expression of tumor suppressor genes. 5-Aza-4'-thio-2'-deoxycytidine (Aza-TdCyd or ATC) is a recently described thiol-substituted DNMTi that has been shown to have anti-tumor activity in solid tumor models. In this study, we investigated the therapeutic potential of ATC in a murine transplantation model of myelodysplastic syndrome. ATC treatment led to the transformation of transplanted wild-type bone marrow nucleated cells into lymphoid leukemia, and healthy mice treated with ATC also developed lymphoid leukemia. Whole-exome sequencing revealed 1,000 acquired mutations, almost all of which were C>G transversions in a specific 5'-NCG-3' context. These mutations involved dozens of genes involved in human lymphoid leukemia, such as Notch1, Pten, Pax5, Trp53, and Nf1. Human cells treated in vitro with ATC showed 1,000 acquired C>G transversions in a similar context. Deletion of Dck, the rate-limiting enzyme for the cytidine salvage pathway, eliminated C>G transversions. Taken together, these findings demonstrate a highly penetrant mutagenic and leukemogenic phenotype associated with ATC. Significance: Treatment with a DNA methyltransferase inhibitor generates a distinct mutation signature and triggers leukemic transformation, which has important implications for the research and clinical applications of these inhibitors.
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Affiliation(s)
- Ryan M. Bertoli
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Michael J. Difilippantonio
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Anthony Wokasch
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Madison R.B. Marasco
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Haley Klimaszewski
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Susannah Gammell
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yuelin J. Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Robert L. Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Dengchao Cao
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Matthew J. Walter
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Peter D. Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
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7
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Hou BY, Wu MH, Hsu HY, Lin YC, Yang DI. Polysaccharides from Basella alba Protect Post-Mitotic Neurons against Cell Cycle Re-Entry and Apoptosis Induced by the Amyloid-Beta Peptide by Blocking Sonic Hedgehog Expression. Int J Mol Sci 2024; 25:7316. [PMID: 39000427 PMCID: PMC11242684 DOI: 10.3390/ijms25137316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
The amyloid-beta peptide (Aβ) is the neurotoxic component in senile plaques of Alzheimer's disease (AD) brains. Previously we have reported that Aβ toxicity is mediated by the induction of sonic hedgehog (SHH) to trigger cell cycle re-entry (CCR) and apoptosis in post-mitotic neurons. Basella alba is a vegetable whose polysaccharides carry immunomodulatory and anti-cancer actions, but their protective effects against neurodegeneration have never been reported. Herein, we tested whether polysaccharides derived from Basella alba (PPV-6) may inhibit Aβ toxicity and explored its underlying mechanisms. In differentiated rat cortical neurons, Aβ25-35 reduced cell viability, damaged neuronal structure, and compromised mitochondrial bioenergetic functions, all of which were recovered by PPV-6. Immunocytochemistry and western blotting revealed that Aβ25-35-mediated induction of cell cycle markers including cyclin D1, proliferating cell nuclear antigen (PCNA), and histone H3 phosphorylated at Ser-10 (p-Histone H3) in differentiated neurons was all suppressed by PPV-6, along with mitigation of caspase-3 cleavage. Further studies revealed that PPV-6 inhibited Aβ25-35 induction of SHH; indeed, PPV-6 was capable of suppressing neuronal CCR and apoptosis triggered by the exogenous N-terminal fragment of sonic hedgehog (SHH-N). Our findings demonstrated that, in the fully differentiated neurons, PPV-6 exerts protective actions against Aβ neurotoxicity via the downregulation of SHH to suppress neuronal CCR and apoptosis.
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Affiliation(s)
- Bo-Yu Hou
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (B.-Y.H.); (M.-H.W.)
| | - Ming-Hsuan Wu
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (B.-Y.H.); (M.-H.W.)
| | - Hui-Yu Hsu
- Mynature Biotech Inc., Yilan 260021, Taiwan;
| | - Yi-Chun Lin
- Department of Neurology, Taipei City Hospital Renai Branch, Taipei 106243, Taiwan
| | - Ding-I Yang
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan; (B.-Y.H.); (M.-H.W.)
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
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8
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Gok B, Budama-Kilinc Y, Kecel-Gunduz S. Anti-aging activity of Syn-Ake peptide by in silico approaches and in vitro tests. J Biomol Struct Dyn 2024; 42:5015-5029. [PMID: 37349941 DOI: 10.1080/07391102.2023.2223681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
The increase in the aging population worldwide has led scientists to turn to research to prevent the aging process. In this context, synthetic peptides emerge as candidate molecules for developing new anti-aging products. This study aims to investigate the possible interactions of Syn-Ake, a synthetic peptide, with matrix metalloproteinases (MMPs) and Sirtuin 1 (SIRT1), which are the targets of anti-aging activities with in silico approaches, and to determine the antioxidant activity, and safety profile of the peptide by in vitro methods such as cytotoxicity (MTT) and genotoxicity (Ames) tests. The molecular docking study showed that the docking score energy of MMP receptors was in the order of MMP-13 < MMP-8 < MMP-1. Syn-Ake peptide provided the lowest and the most stable binding to the SIRT1 receptor at -9.32 kcal/mol. Binding interaction and protein-ligand stability of Syn-Ake with MMPs and SIRT1 in a dynamic system were predicted by 50 ns molecular dynamic (MD) simulation studies. The MD results showed that the Syn-Ake peptide remained stable in the active site of MMP-13 and SIRT1 receptors during 50 ns simulations. In addition, the antioxidant activity of Syn-Ake was investigated using diphenyl-2-picril-hydrazine (DPPH) method since it is crucial to remove free radicals that are effective in skin aging. The results revealed the concentration-dependent increased DPPH radical scavenging activity of the peptide. Finally, the safety of the Syn-Ake was investigated, and the safe dose of the peptide was determined. In conclusion, in silico and in vitro analyses show that the Syn-Ake peptide may hold promise in anti-aging formulations with its high efficacy and safety profile.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bahar Gok
- Graduate School of Natural and Applied Science, Yildiz Technical University, Istanbul, Turkey
| | - Yasemin Budama-Kilinc
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Serda Kecel-Gunduz
- Faculty of Science, Department of Physics, Istanbul University, Istanbul, Turkey
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9
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Fu F, Li X, Chen Y, Li L, Dou J, Liang K, Chen Y, Lu Y, Huang Y. Genotoxicity and cytotoxicity evaluation of a heat-not-burn product. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 897:503784. [PMID: 39054007 DOI: 10.1016/j.mrgentox.2024.503784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 07/27/2024]
Abstract
'Heat-not-burn' products (HnBP) contain lower levels of harmful substances than traditional cigarettes, but the use of these products warrants further toxicological evaluation. We have compared the cytotoxicity and genotoxicity of a heat-not burn product with conventional cigarettes, in vivo and in vitro. Male Sprague Dawley rats were exposed to mainstream smoke from conventional cigarettes or a HnBP, for 4 or 28 days, followed by isolation of bone marrow polychromatic erythrocytes (PCE) and histological examination of the testes. Chinese hamster lung fibroblast cells were exposed in vitro to total particulate matter from cigarette smoke obtained through Cambridge filters. The cytotoxicity and genotoxicity of total particulate matter were assessed by the neutral red uptake assay, chromosome aberration assay, in vitro micronucleus test, comet assay, and Ames assay. In the short-term exposure rat models, only the conventional-cigarettes group showed a significant increase in the ratio of micronuclei to total PCE. There was no significant difference in rat testis histology in the long-term exposure models. In vitro, in the neutral red uptake assay, the HnBP product showed lower cytotoxicity than conventional cigarettes. Conventional cigarettes showed greater genotoxicity in the chromosome aberration assay, high-dose Ames tests with exogenous metabolic activation, and micronucleus tests. In summary, our results suggest that HnBP have lower cytotoxicity and genotoxicity than conventional cigarettes.
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Affiliation(s)
- Fudong Fu
- Department of Pulmonary and Critical Care Medicine, and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyu Li
- Department of Pulmonary and Critical Care Medicine, and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Younan Chen
- Department of Pulmonary and Critical Care Medicine, and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Key Laboratory of Transplant Engineering and Immunology, NHFPC, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lan Li
- Key Laboratory of Transplant Engineering and Immunology, NHFPC, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiexiong Dou
- Sichuan Center for Disease Control and Prevention, Chengdu 610044, China
| | - Kun Liang
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, Chengdu 610101, China; New Tobacco Products Engineering and Technology Research Center of Sichuan Province, Chengdu 610101 China
| | - Yexian Chen
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, Chengdu 610101, China; New Tobacco Products Engineering and Technology Research Center of Sichuan Province, Chengdu 610101 China
| | - Yanrong Lu
- Key Laboratory of Transplant Engineering and Immunology, NHFPC, Regenerative Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuchuan Huang
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, Chengdu 610101, China; New Tobacco Products Engineering and Technology Research Center of Sichuan Province, Chengdu 610101 China.
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Amorim AM, Piochi LF, Gaspar AT, Preto A, Rosário-Ferreira N, Moreira IS. Advancing Drug Safety in Drug Development: Bridging Computational Predictions for Enhanced Toxicity Prediction. Chem Res Toxicol 2024; 37:827-849. [PMID: 38758610 PMCID: PMC11187637 DOI: 10.1021/acs.chemrestox.3c00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
The attrition rate of drugs in clinical trials is generally quite high, with estimates suggesting that approximately 90% of drugs fail to make it through the process. The identification of unexpected toxicity issues during preclinical stages is a significant factor contributing to this high rate of failure. These issues can have a major impact on the success of a drug and must be carefully considered throughout the development process. These late-stage rejections or withdrawals of drug candidates significantly increase the costs associated with drug development, particularly when toxicity is detected during clinical trials or after market release. Understanding drug-biological target interactions is essential for evaluating compound toxicity and safety, as well as predicting therapeutic effects and potential off-target effects that could lead to toxicity. This will enable scientists to predict and assess the safety profiles of drug candidates more accurately. Evaluation of toxicity and safety is a critical aspect of drug development, and biomolecules, particularly proteins, play vital roles in complex biological networks and often serve as targets for various chemicals. Therefore, a better understanding of these interactions is crucial for the advancement of drug development. The development of computational methods for evaluating protein-ligand interactions and predicting toxicity is emerging as a promising approach that adheres to the 3Rs principles (replace, reduce, and refine) and has garnered significant attention in recent years. In this review, we present a thorough examination of the latest breakthroughs in drug toxicity prediction, highlighting the significance of drug-target binding affinity in anticipating and mitigating possible adverse effects. In doing so, we aim to contribute to the development of more effective and secure drugs.
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Affiliation(s)
- Ana M.
B. Amorim
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- PhD
Programme in Biosciences, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- PURR.AI,
Rua Pedro Nunes, IPN Incubadora, Ed C, 3030-199 Coimbra, Portugal
| | - Luiz F. Piochi
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Ana T. Gaspar
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António
J. Preto
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- PhD Programme
in Experimental Biology and Biomedicine, Institute for Interdisciplinary
Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
| | - Nícia Rosário-Ferreira
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Irina S. Moreira
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-UC—Center
for Neuroscience and Cell Biology, University
of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CIBB—Centre
for Innovative Biomedicine and Biotechnology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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11
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Maliwal D, Pissurlenkar RRS, Telvekar V. Comprehensive computational study in the identification of novel potential cholesterol lowering agents targeting proprotein convertase subtilisin/kexin type 9. J Biomol Struct Dyn 2024; 42:4656-4667. [PMID: 37309035 DOI: 10.1080/07391102.2023.2222173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/30/2023] [Indexed: 06/14/2023]
Abstract
The enzymatic target proprotein convertase subtilisin/kexin type 9 (PCSK9) is critically involved in the regulation of the lipoprotein metabolism leading to the degradation of low-density lipoprotein receptors (LDLRs) upon binding. Drugs that lower LDL cholesterol (LDL-C) through the inhibition of PCSK9 are useful in the management of hypercholesterolemia which greatly reduces the associated risk of atherosclerotic cardiovascular disease (CVD). In 2015, anti-PCSK9 monoclonal antibodies (mAbs), alirocumab and evolocumab were approved but owing to their high costs their prior authorization practices were impeded, reducing their long-term adherence. This has drawn considerable attention for the development of small-molecule PCSK9 inhibitors. In this research work, novel and diverse molecules with affinity towards PCSK9 thereby having ability to lower cholesterol. A hierarchical multistep docking was implemented to identify small molecules from chemical libraries with a score cutoff -8.00 kcal/mol, thereby weeding all the non-potential molecules. A set of seven representative molecules Z1139749023, Z1142698190, Z2242867634, Z2242893449, Z2242894417, Z2242909019, and Z2242914794 have been identified from a comprehensive computational study which included assessment of pharmacokinetics and toxicity profiles and binding interactions along with in-depth analysis of structural dynamics and integrity using prolong molecular dynamics (MD) simulation (in-duplicate). Furthermore the binding affinity of these PCSK9 inhibitory candidates molecules was ascertained over 1000 trajectory frames using MM-GBSA calculations. The molecules reported herein are propitious candidates for further development through necessary experimental considerations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deepika Maliwal
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | | | - Vikas Telvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
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Thomas DN, Wills JW, Tracey H, Baldwin SJ, Burman M, Williams AN, Harte DSG, Buckley RA, Lynch AM. Ames test study designs for nitrosamine mutagenicity testing: qualitative and quantitative analysis of key assay parameters. Mutagenesis 2024; 39:78-95. [PMID: 38112628 DOI: 10.1093/mutage/gead033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023] Open
Abstract
The robust control of genotoxic N-nitrosamine (NA) impurities is an important safety consideration for the pharmaceutical industry, especially considering recent drug product withdrawals. NAs belong to the 'cohort of concern' list of genotoxic impurities (ICH M7) because of the mutagenic and carcinogenic potency of this chemical class. In addition, regulatory concerns exist regarding the capacity of the Ames test to predict the carcinogenic potential of NAs because of historically discordant results. The reasons postulated to explain these discordant data generally point to aspects of Ames test study design. These include vehicle solvent choice, liver S9 species, bacterial strain, compound concentration, and use of pre-incubation versus plate incorporation methods. Many of these concerns have their roots in historical data generated prior to the harmonization of Ames test guidelines. Therefore, we investigated various Ames test assay parameters and used qualitative analysis and quantitative benchmark dose modelling to identify which combinations provided the most sensitive conditions in terms of mutagenic potency. Two alkyl-nitrosamines, N-nitrosodimethylamine (NDMA) and N-nitrosodiethylamine (NDEA) were studied. NDMA and NDEA mutagenicity was readily detected in the Ames test and key assay parameters were identified that contributed to assay sensitivity rankings. The pre-incubation method (30-min incubation), appropriate vehicle (water or methanol), and hamster-induced liver S9, alongside Salmonella typhimurium strains TA100 and TA1535 and Escherichia coli strain WP2uvrA(pKM101) provide the most sensitive combination of assay parameters in terms of NDMA and NDEA mutagenic potency in the Ames test. Using these parameters and further quantitative benchmark dose modelling, we show that N-nitrosomethylethylamine (NMEA) is positive in Ames test and therefore should no longer be considered a historically discordant NA. The results presented herein define a sensitive Ames test design that can be deployed for the assessment of NAs to support robust impurity qualifications.
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Affiliation(s)
- Dean N Thomas
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - John W Wills
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - Helen Tracey
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - Sandy J Baldwin
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - Mark Burman
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - Abbie N Williams
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - Danielle S G Harte
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - Ruby A Buckley
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
| | - Anthony M Lynch
- GSK Research & Development, Genetic Toxicology and Photosafety, Stevenage SG1 2NY, United Kingdom
- School of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, United Kingdom
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Pescke IK, de Oliveira Rozino L, Zenato K, Cardozo T, Flores WH, Vargas VMF. Lowering the pH leads to the disaggregation of NiO and ZnO nanoparticles and modifies the mutagenic response. J Appl Toxicol 2024; 44:445-454. [PMID: 37828814 DOI: 10.1002/jat.4553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
In a changing environmental scenario, acid rain can have a significant impact on aquatic ecosystems. Acidification is known to produce corrosion in metals, hence increasing their harmful effects on the environment, organisms and human health. The prevalent use of metallic nanoparticles (NPs) in everyday products raises concerns regarding exposure and nanotoxicity even in these acidified conditions. We thus report on the cytotoxic and genotoxic potential of nickel oxide (NiO-NP) and zinc oxide (ZnO-NP) NPs when suspended in aqueous media in light of pH variations (7.5 and 5). A modified microsuspension method of the Salmonella/microsome assay was adopted, and strains (TA97a, TA98, TA100, TA102) were exposed to NPs (10-1280 μg/plate) with and without a metabolization fraction. The acidic condition favored disaggregation and caused a decrease in NPs size. Mutagenicity was observed in all samples and different strains, with greater DNA base pair substitution damage (TA100 and TA102), but extrinsic conditions (pH) suggest different action mechanisms of NiO-NP and ZnO-NP on genetic content. Mutagenic activity was found to increase upon metabolic activation (TA98, TA100, and TA102) demonstrating the bioactivity of NiO-NP and ZnO-NP in relation to metabolites generated by the mammalian p450 system in vitro. Modifications in the Salmonella assay methodology increased cell exposure time. The observed responses recommend this modified assay as one of the methodologies of choice for nanoecotoxicological evaluation. These findings emphasize the significance of incorporating the environmental context when evaluating the toxicity of metal-based NPs.
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Affiliation(s)
- Ismael Krüger Pescke
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lívia de Oliveira Rozino
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Karoline Zenato
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Tatiane Cardozo
- Grupo de Materiais Nanoestruturados, Universidade Federal do Pampa (UNIPAMPA), Bagé, Brazil
| | | | - Vera Maria Ferrão Vargas
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Mutagênese Ambiental, Centro de Ecologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Abbasi Z, Ghasemi SM, Ahmadi Y, Shokri D. Isolation and Identification of Effective Probiotics on Drug-Resistant Acinetobacter baumannii Strains and Their Biofilms. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:8570521. [PMID: 38440403 PMCID: PMC10911883 DOI: 10.1155/2024/8570521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/14/2024] [Accepted: 01/22/2024] [Indexed: 03/06/2024]
Abstract
Introduction This study aimed to identify, assess, and isolate strong lactobacilli demonstrating broad antibacterial and anti-biofilm activity against drug-resistant strains of Acinetobacter baumannii. Additionally, the mechanism of inhibition of these organisms was to be determined. Methods Over a 6-month period (from December 2021 to June 2022), 53 clinical A. baumannii strains were collected from clinical samples. Twenty probiotic strains were isolated from local dairy products. Antibacterial activity of Lactobacillus strains' cell-free supernatant (CFS) was identified using the agar well diffusion method and the microbroth dilution test. Anti-biofilm effect was performed by the microtiter plate assay. The MTT assay was also used to look into the probiotics' cytotoxic effects on the L929 fibroblast cell line. Results During the 6-month period, 53 clinical A. baumannii strains were obtained and identified. Out of 20 lactobacillus strains, the CFS of a lactobacillus strain (named L9) showed an inhibitory effect against all A. baumannii strains. Using the broth microdilution method, it was shown that the minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of CFS extracts of L9 strains against A. baumannii strains were both ¼ mg/mL. The result of the anti-biofilm showed that the selected probiotic could inhibit biofilm formation. The most common organic acid produced by all Lactobacillus strains, according to the HPLC method, was lactic acid, which was followed by acetic acid. The L929 fibroblast cell line was used in the cytotoxicity assay, which revealed that 100% of the cells in the L929 fibroblast cell line survived treatment with successive doses of CFSs for a full day. Conclusion The probiotic strain isolated from local yogurt in this study showed potential anti-biofilm and antimicrobial properties against all drug-resistant Acinetobacter isolates. Given the increasing interest in probiotic microorganisms based on their high health benefits, further studies are recommended on the mechanisms of action between probiotics and A. baumannii strains to find new solutions for biological control and treatment of these infections without the use of antibiotics.
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Affiliation(s)
- Zahra Abbasi
- Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Seyed Mahdi Ghasemi
- Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Yasaman Ahmadi
- Department of Microbiology, Kish International Branch of Islamic Azad University, Kish, Iran
| | - Dariush Shokri
- Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
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Spiliotopoulos D, Koelbert C, Audebert M, Barisch I, Bellet D, Constans M, Czich A, Finot F, Gervais V, Khoury L, Kirchnawy C, Kitamoto S, Le Tesson A, Malesic L, Matsuyama R, Mayrhofer E, Mouche I, Preikschat B, Prielinger L, Rainer B, Roblin C, Wäse K. Assessment of the performance of the Ames MPF™ assay: A multicenter collaborative study with six coded chemicals. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 893:503718. [PMID: 38272629 DOI: 10.1016/j.mrgentox.2023.503718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/19/2023] [Indexed: 01/27/2024]
Abstract
The Ames MPF™ is a miniaturized, microplate fluctuation format of the Ames test. It is a standardized, commercially available product which can be used to assess mutagenicity in Salmonella and E. coli strains in 384-well plates using a color change-based readout. Several peer-reviewed comparisons of the Ames MPF™ to the Ames test in Petri dishes confirmed its suitability to evaluate the mutagenic potential of a variety of test items. An international multicenter study involving seven laboratories tested six coded chemicals with this assay using five bacterial strains, as recommended by the OECD test guideline 471. The data generated by the participating laboratories was in excellent agreement (93%), and the similarity of their dose response curves, as analyzed with sophisticated statistical approaches further confirmed the suitability of the Ames MPF™ assay as an alternative to the Ames test on agar plates, but with advantages with respect to significantly reduced amount of test substance and S9 requirements, speed, hands-on time and, potentially automation.
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Affiliation(s)
| | | | - Marc Audebert
- PrediTox, 1 place Pierre Potier, 31100 Toulouse, France; INRAE UMR1331 Toxalim, 180 chemin de Tournefeuille, 31300 Toulouse, France
| | - Ilona Barisch
- Genetic Toxicology, Preclinical Safety, Sanofi-Aventis Deutschland GmbH, 65926 Frankfurt am Main, Germany
| | - Deborah Bellet
- GenEvolutioN, 2, 8 Rue de Rouen, 78440 Porcheville, France
| | | | - Andreas Czich
- Genetic Toxicology, Preclinical Safety, Sanofi-Aventis Deutschland GmbH, 65926 Frankfurt am Main, Germany
| | - Francis Finot
- GenEvolutioN, 2, 8 Rue de Rouen, 78440 Porcheville, France
| | - Véronique Gervais
- Servier Group, Non-Clinical Safety Department, F-45403 Orléans-Gidy, France
| | - Laure Khoury
- PrediTox, 1 place Pierre Potier, 31100 Toulouse, France
| | - Christian Kirchnawy
- OFI, Austrian Research Institute for Chemistry and Technology, Department for Microbiology and Cell Culture, Franz-Grill Straße 5, Objekt 213, 1030 Vienna, Austria
| | - Sachiko Kitamoto
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugadenaka 3-chome, konohana-ku, Osaka, Japan
| | - Audrey Le Tesson
- Servier Group, Non-Clinical Safety Department, F-45403 Orléans-Gidy, France
| | - Laure Malesic
- GenEvolutioN, 2, 8 Rue de Rouen, 78440 Porcheville, France
| | - Ryoko Matsuyama
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 1-98, Kasugadenaka 3-chome, konohana-ku, Osaka, Japan
| | - Elisa Mayrhofer
- OFI, Austrian Research Institute for Chemistry and Technology, Department for Microbiology and Cell Culture, Franz-Grill Straße 5, Objekt 213, 1030 Vienna, Austria
| | | | - Birgit Preikschat
- Genetic Toxicology, Preclinical Safety, Sanofi-Aventis Deutschland GmbH, 65926 Frankfurt am Main, Germany
| | - Lukas Prielinger
- Department of Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Favoritenstraße 222, 1100 Vienna, Austria
| | - Bernhard Rainer
- Department of Applied Life Sciences, University of Applied Sciences, FH Campus Wien, Favoritenstraße 222, 1100 Vienna, Austria
| | - Clémence Roblin
- Servier Group, Non-Clinical Safety Department, F-45403 Orléans-Gidy, France
| | - Kerstin Wäse
- Genetic Toxicology, Preclinical Safety, Sanofi-Aventis Deutschland GmbH, 65926 Frankfurt am Main, Germany
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Aplan P, Bertoli R, Chung YJ, Difilippantonio M, Wokasch A, Marasco M, Klimaszewski H, Garber S, Zhu Y, Walker R, Cao D, Doroshow J, Meltzer P. 5-Aza-4'-thio-2'-deoxycytidine induces C>G transversions in a specific trinucleotide context and leads to acute lymphoid leukemia. RESEARCH SQUARE 2023:rs.3.rs-3186246. [PMID: 38168433 PMCID: PMC10760231 DOI: 10.21203/rs.3.rs-3186246/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DNA methyltransferase inhibitors (DNMTi), most commonly cytidine analogs, are compounds that are used clinically to decrease 5'-cytosine methylation, with the aim of re-expression of tumor suppressor genes. We used a murine pre-clinical model of myelodysplastic syndrome based on transplantation of cells expressing a NUP98::HOXD13 transgene to investigate 5-Aza-4'-thio-2'-deoxycytidine (Aza TdCyd or ATC), a thiol substituted DNMTi, as a potential therapy. We found that ATC treatment led to lymphoid leukemia in wild-type recipient cells; further study revealed that healthy mice treated with ATC also developed lymphoid leukemia. Whole exome sequencing revealed thousands of acquired mutations, almost all of which were C > G transversions in a previously unrecognized, specific 5'-NCG-3' context. These mutations involved dozens of genes well-known to be involved in human lymphoid leukemia, such as Notch1, Pten, Pax5, Trp53 , and Nf1 . Treatment of human cells in vitro showed thousands of acquired C > G transversions in a similar context. Deletion of Dck , the rate-limiting enzyme for the cytidine salvage pathway, eliminated C > G transversions. Taken together, these findings demonstrate that DNMTi can be potent mutagens in human and mouse cells, both in vitro and in vivo .
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Beal MA, Chen G, Dearfield KL, Gi M, Gollapudi B, Heflich RH, Horibata K, Long AS, Lovell DP, Parsons BL, Pfuhler S, Wills J, Zeller A, Johnson G, White PA. Interpretation of in vitro concentration-response data for risk assessment and regulatory decision-making: Report from the 2022 IWGT quantitative analysis expert working group meeting. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2023. [PMID: 38115239 DOI: 10.1002/em.22582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/15/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Quantitative risk assessments of chemicals are routinely performed using in vivo data from rodents; however, there is growing recognition that non-animal approaches can be human-relevant alternatives. There is an urgent need to build confidence in non-animal alternatives given the international support to reduce the use of animals in toxicity testing where possible. In order for scientists and risk assessors to prepare for this paradigm shift in toxicity assessment, standardization and consensus on in vitro testing strategies and data interpretation will need to be established. To address this issue, an Expert Working Group (EWG) of the 8th International Workshop on Genotoxicity Testing (IWGT) evaluated the utility of quantitative in vitro genotoxicity concentration-response data for risk assessment. The EWG first evaluated available in vitro methodologies and then examined the variability and maximal response of in vitro tests to estimate biologically relevant values for the critical effect sizes considered adverse or unacceptable. Next, the EWG reviewed the approaches and computational models employed to provide human-relevant dose context to in vitro data. Lastly, the EWG evaluated risk assessment applications for which in vitro data are ready for use and applications where further work is required. The EWG concluded that in vitro genotoxicity concentration-response data can be interpreted in a risk assessment context. However, prior to routine use in regulatory settings, further research will be required to address the remaining uncertainties and limitations.
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Affiliation(s)
- Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Guangchao Chen
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Utrecht, the Netherlands
| | - Kerry L Dearfield
- Retired from US Environmental Protection Agency and US Department of Agriculture, Washington, DC, USA
| | - Min Gi
- Department of Environmental Risk Assessment, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | | | - Robert H Heflich
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Katsuyoshi Horibata
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- St George's Medical School, University of London, London, UK
| | - Barbara L Parsons
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Stefan Pfuhler
- Global Product Stewardship - Human Safety, Procter & Gamble, Cincinnati, Ohio, USA
| | - John Wills
- Genetic Toxicology and Photosafety, GSK Research & Development, Stevenage, UK
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George Johnson
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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Lugo L, Venegas C, Guarin Trujillo E, Diaz Granados-Ramírez MA, Martin A, Vesga FJ, Pérez-Flórez A, Celis C. Ecotoxicology Evaluation of a Fenton-Type Process Catalyzed with Lamellar Structures Impregnated with Fe or Cu for the Removal of Amoxicillin and Glyphosate. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:7172. [PMID: 38131723 PMCID: PMC10743043 DOI: 10.3390/ijerph20247172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/10/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Antibiotics and pesticides, as well as various emerging contaminants that are present in surface waters, raise significant environmental concerns. Advanced oxidation processes, which are employed to eliminate these substances, have demonstrated remarkable effectiveness. However, during the degradation process, by-products that are not completely mineralized are generated, posing a substantial risk to aquatic ecosystem organisms; therefore, it is crucial to assess effluent ecotoxicity following treatment. This study aimed to assess the toxicity of effluents produced during the removal of amoxicillin and glyphosate with a Fenton-type process using a laminar structure catalyzed with iron (Fe) and copper (Cu). The evaluation included the use of Daphnia magna, Selenastrum capricornutum, and Lactuca sativa, and mutagenicity testing was performed using strains TA98 and TA100 of Salmonella typhimurium. Both treated and untreated effluents exhibited inhibitory effects on root growth in L. sativa, even at low concentrations ranging from 1% to 10% v/v. Similarly, negative impacts on the growth of algal cells of S. capricornutum were observed at concentrations as low as 0.025% v/v, particularly in cases involving amoxicillin-copper (Cu) and glyphosate with copper (Cu) and iron (Fe). Notably, in the case of D. magna, mortality was noticeable even at concentrations of 10% v/v. Additionally, the treatment of amoxicillin with double-layer hydroxides of Fe and Cu resulted in mutagenicity (IM ≥ 2.0), highlighting the necessity to treat the effluent further from the advanced oxidation process to reduce ecological risks.
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Affiliation(s)
- Lorena Lugo
- Department of Chemistry, Research Line in Environmental and Materials Technology (ITAM), Pontificia Universidad Javeriana, Carrera 7 No. 43–82, Bogotá 110231, Colombia; (L.L.); (A.M.); (A.P.-F.)
| | - Camilo Venegas
- Department of Microbiology, School of Sciences, Microbiological Quality of Water and Sludge (CMAL), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá 110231, Colombia; (C.V.); (E.G.T.); (M.A.D.G.-R.); (F.-J.V.)
| | - Elizabeth Guarin Trujillo
- Department of Microbiology, School of Sciences, Microbiological Quality of Water and Sludge (CMAL), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá 110231, Colombia; (C.V.); (E.G.T.); (M.A.D.G.-R.); (F.-J.V.)
| | - Maria Alejandra Diaz Granados-Ramírez
- Department of Microbiology, School of Sciences, Microbiological Quality of Water and Sludge (CMAL), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá 110231, Colombia; (C.V.); (E.G.T.); (M.A.D.G.-R.); (F.-J.V.)
| | - Alison Martin
- Department of Chemistry, Research Line in Environmental and Materials Technology (ITAM), Pontificia Universidad Javeriana, Carrera 7 No. 43–82, Bogotá 110231, Colombia; (L.L.); (A.M.); (A.P.-F.)
| | - Fidson-Juarismy Vesga
- Department of Microbiology, School of Sciences, Microbiological Quality of Water and Sludge (CMAL), Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá 110231, Colombia; (C.V.); (E.G.T.); (M.A.D.G.-R.); (F.-J.V.)
| | - Alejandro Pérez-Flórez
- Department of Chemistry, Research Line in Environmental and Materials Technology (ITAM), Pontificia Universidad Javeriana, Carrera 7 No. 43–82, Bogotá 110231, Colombia; (L.L.); (A.M.); (A.P.-F.)
| | - Crispín Celis
- Department of Chemistry, Research Line in Environmental and Materials Technology (ITAM), Pontificia Universidad Javeriana, Carrera 7 No. 43–82, Bogotá 110231, Colombia; (L.L.); (A.M.); (A.P.-F.)
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Yamada M, Suzuki T, Kohara A, Honma M. Carcinogenic risk of food additive AF-2 banned in Japan: a case study on reassessment of genotoxicity. Genes Environ 2023; 45:33. [PMID: 38053221 PMCID: PMC10696715 DOI: 10.1186/s41021-023-00292-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Carcinogenic risk assessment studies have been repeatedly improved and are still being debated to find a goal. Evaluation might be changed if new approaches would be applied to some chemicals which means that new approaches may change the final assessment. In this paper, the risk assessment of a chemical, in particular the proper carcinogenicity, is examined using the long-banned food additive, 2-(2-furyl)-3-(5-nitro-2-furyl)-acrylamide, AF-2, as a case study. RESULTS First, Ames tests were carried out using strains TA1535, TA100, TA1538, and TA98 and their nitroreductase-deficient strains YG7127, YG7128, YG7129, and YG7130. The results showed that mutagenic activity was reduced by about 50% in the nitroreductase-deficient strains, indicating that part of the mutagenic activity shown in Ames test was due to bacterial metabolism. Second, in vivo genotoxicity tests were conducted, including the one that had not been developed in 1970's. Both a micronucleus test and a gene mutation assay using transgenic mice were negative. Third, assuming it is a genotoxic carcinogen, the virtual safety dose of 550 μg/day was calculated from the TD50 in rats with a probability of 10-5. CONCLUSION AF-2 has been shown to be carcinogenic to rodents and has previously been indicated to be genotoxic in vitro. However, the present in vivo genotoxicity study, it was negative in the forestomach, a target organ for cancer, particularly in the gene mutation assay in transgenic mice. Considering the daily intake of AF-2 in the 1970s and its virtually safety dose, the carcinogenic risk of AF-2 could be considered acceptable.
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Affiliation(s)
- Masami Yamada
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, Kanagawa, 239-8686, Japan.
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-9501, Japan.
| | - Takayoshi Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-9501, Japan
| | - Arihiro Kohara
- JCRB Cell Bank, National Institute of Biomedical Innovation, 7-6-8, Saito-asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Masamitsu Honma
- Division of General Affairs, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-9501, Japan
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20
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Mishra N, Srivastava R. Bacterial worth in genotoxicity assessment studies. J Microbiol Methods 2023; 215:106860. [PMID: 38008307 DOI: 10.1016/j.mimet.2023.106860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Bacterial-based genotoxicity test systems play a significant role in the detection and evaluation of genotoxicity in vitro and have gained importance due to attributes like wide applicability, speed, high sensitivity, good reproducibility, and simplicity. The Salmonella microsomal mutagenicity assay was created by Ames and colleagues at the beginning of the 1970s, and it was based on the fundamental notion that in auxotrophic bacterial strains with inhibited growth, a mutant gene would revert to its original state on exposure to genotoxicants. This is the most successful and widely used in vitro genotoxicity test. Later, a number of additional test systems that incorporated DNA repair mechanisms including the bacterial SOS response were created. Genetic engineering has further provided significant advancement in these test systems with the development of highly sophisticated bacterial tester strains with significantly increased sensitivity to evaluate the chemical nature of hazardous substances and pollutants. These bacterial bioassays render an opportunity to detect the defined effects of compounds at the molecular level. In this review, all the aspects related to the bacterial system in genotoxicity assessment have been summarized and their role is elaborated concerning real-time requirements and future perspectives.
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Affiliation(s)
- Nidhi Mishra
- Department of Zoology, University of Lucknow, Lucknow, U.P. 226007, India.
| | - Rashmi Srivastava
- Department of Zoology, Babasaheb Bhimrao Ambedkar University, Lucknow, U.P. 226025, India
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21
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Ghiaei A, Ghasemi SM, Shokri D. Investigating the Antagonistic Effect of Indigenous Probiotics on Carbapenem-Resistant Pseudomonas aeruginosa Strains. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6645657. [PMID: 37810624 PMCID: PMC10555497 DOI: 10.1155/2023/6645657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Introduction With the increase of hospital infections due to the indiscriminate use of antibiotics, multidrug resistance has increased, decreasing the effectiveness of antibiotics against these infections. For this reason, the identification of alternative agents such as probiotics has been considered. The aim of this study was to isolate and identify effective probiotics against carbapenem-resistant Pseudomonas aeruginosa strains. Material and Methods. During a period of eight months, isolates of P. aeruginosa were collected from patients in three hospitals in Isfahan. The presence of metallo-beta-lactamase enzymes was determined by the combination disc test (CDT). The inhibitory and antimicrobial activities of 20 probiotic bacteria isolated from local dairy products against these strains were investigated by agar dilution. Two probiotic strains that showed broader inhibition results were selected, and the values of the lowest inhibitory concentration (MIC) and the lowest lethal concentration (MBC) and their antibiofilm effect were determined using the microtiter plate method. The concentration of organic acids was done by HPLC. Findings. Of the 100 samples isolated and identified, 61 samples (61%) exhibited multiple drug resistance (MDR) and were selected for further investigation. Phenotypic diagnosis of the presence of metallo-beta-lactamase enzymes revealed that 74.5% of the strains were positive. The results showed that these two probiotics killed P. aeruginosa strains after only one hour, and the inhibition mechanism was due to the presence of lactic acid and acetic acid. The antibiofilm effect of these two probiotics was at concentrations of 1/2 and 1/4. Conclusion The two Lactobacillus isolates had potential antimicrobial and antibiofilm properties against all carbapenem-resistant P. aeruginosa strains, even at thinner dilutions. Considering the broad activity of this strain, it can potentially be used for biocontrol of these strains.
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Affiliation(s)
- Azita Ghiaei
- Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Seyed Mahdi Ghasemi
- Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Dariush Shokri
- Nosocomial Infection Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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22
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Feeney SV, Lui R, Guan D, Matthews S. Multiple Instance Learning Improves Ames Mutagenicity Prediction for Problematic Molecular Species. Chem Res Toxicol 2023; 36:1227-1237. [PMID: 37477941 DOI: 10.1021/acs.chemrestox.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The prediction of Ames mutagenicity continues to be a concern in both regulatory and pharmacological toxicology. Traditional quantitative structure-activity relationship (QSAR) models of mutagenicity make predictions based on molecular descriptors calculated on a chemical data set used in their training. However, it is known that molecules such as aromatic amines can be non-mutagenic themselves but metabolically activated by S9 rodent liver enzyme in Ames tests forming molecules such as iminoquinones or amine substituents that better stabilize mutagenic nitrenium ions in known pathways of mutagenicity. Modern in silico modeling methods can implicitly model these metabolites through consideration of the structural elements relevant to their formation but do not include explicit modeling of these metabolites' potential activity. These metabolites do not have a known individual mutagenicity label and, in their current state, cannot be fitted into a traditional QSAR model. Multiple instance learning (MIL) however can be applied to a group of metabolites and their parent under a single mutagenicity label. Here we trained MIL models on Ames data, first with an aromatic amines data set (n = 457), a class known to require metabolic activation, and subsequently on a larger data set (n = 6505) incorporating multiple molecular species. MIL was shown to be able to predict Ames mutagenicity with performance in line with previously established models (balanced accuracy = 0.778), suggesting its potential utility in Ames prediction applications. Furthermore, the MIL model predicted well on identified hard-to-predict molecule groups relative to the models in which these molecule groups were identified. These results are presumably due to the increased consideration of the metabolic contribution to the mutagenic outcome. Further exploration of MIL as a supplement to existing models could aid in the prediction of chemicals where implicit modeling of metabolites cannot fully grasp their characteristics. This paper demonstrates the potential of an MIL approach to modeling Ames tests with S9 and is particularly relevant to metabolically activated xenobiotic mutagens.
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Affiliation(s)
- Samuel V Feeney
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Raymond Lui
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Davy Guan
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Slade Matthews
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
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23
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Lui R, Guan D, Matthews S. Mechanistic Task Groupings Enhance Multitask Deep Learning of Strain-Specific Ames Mutagenicity. Chem Res Toxicol 2023; 36:1248-1254. [PMID: 37478285 DOI: 10.1021/acs.chemrestox.2c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
The Ames test is a gold standard mutagenicity assay that utilizes various Salmonella typhimurium strains with and without S9 fraction to provide insights into the mechanisms by which a chemical can mutate DNA. Multitask deep learning is an ideal framework for developing QSAR models with multiple end points, such as the Ames test, as the joint training of multiple predictive tasks may synergistically improve the prediction accuracy of each task. This work investigated how toxicology domain knowledge can be used to handcraft task groupings that better guide the training of multitask neural networks compared to a naïve ungrouped multitask neural network developed on a complete set of tasks. Sixteen S. typhimurium ± S9 strain tasks were used to generate groupings based on mutagenic and metabolic mechanisms that were reflected in correlation data analyses. Both grouped and ungrouped multitask neural networks predicted the 16 strain tasks with a higher balanced accuracy compared with single task controls, with grouped multitask neural networks consistently featuring incremental increases in predictivity over the ungrouped approach. We conclude that the main variable driving these performance improvements is the general multitask effect with mechanistic task groupings acting as an enhancement step to further concentrate synergistic training signals united by a common biological mechanism. This approach enables incorporation of toxicology domain knowledge into multitask QSAR model development allowing for more transparent and accurate Ames mutagenicity prediction.
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Affiliation(s)
- Raymond Lui
- Computational Pharmacology and Toxicology Laboratory, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Davy Guan
- Computational Pharmacology and Toxicology Laboratory, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Slade Matthews
- Computational Pharmacology and Toxicology Laboratory, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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24
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Su YH, Wu JS, Dai YZ, Chen YT, Lin YX, Tzeng YM, Liao JW. Anti-Oxidant, Anti-Mutagenic Activity and Safety Evaluation of Antrocin. TOXICS 2023; 11:547. [PMID: 37368647 DOI: 10.3390/toxics11060547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023]
Abstract
Antrocin is a novel compound isolated from Antrodia cinnamomea, and is classified as a sesquiterpene lactone. The therapeutic efficacy of antrocin has been studied, and it has shown an antiproliferative effect on various cancers. The aim of this study was to evaluate the anti-oxidant activity, potential genotoxicity, and oral toxicity of antrocin. Ames tests with five different strains of Salmonella typhimurium, chromosomal aberration tests in CHO-K1 cells, and micronucleus tests in ICR mice were conducted. The results of anti-oxidant capacity assays showed that antrocin has great anti-oxidant activity and is a moderately strong antimutagenic agent. In the results of the genotoxicity assays, antrocin did not show any mutagenic potential. In the 28-day oral toxicity test, Sprague Dawley rats were gavaged with 7.5 or 37.5 mg/kg of antrocin for 28 consecutive days. In addition, 7.5 mg/kg sorafenib, an anti-cancer drug, was used as a positive control for toxicity comparison. At the end of the study, antrocin did not produce any toxic effects according to hematology, serum chemistry, urine analysis, or histopathological examinations. According to the results of the genotoxicity and 28-day oral toxicity study, antrocin, at a dose of 37.5 mg/kg, did not cause adverse effects and can be a reference dose for therapeutic agents in humans.
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Affiliation(s)
- Yi-Hui Su
- Graduate Institute of Veterinary Pathobiology, National Chung Hsing University, Taichung 402, Taiwan
| | - Jia-Shuan Wu
- Graduate Institute of Food Safety, National Chung Hsing University, Taichung 402, Taiwan
| | - Yan-Zhen Dai
- Research Center for Animal Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Yng-Tay Chen
- Graduate Institute of Food Safety, National Chung Hsing University, Taichung 402, Taiwan
| | - Yan-Xiu Lin
- Graduate Institute of Veterinary Pathobiology, National Chung Hsing University, Taichung 402, Taiwan
| | - Yew-Min Tzeng
- Department of Applied Science, National Taitung University, Taitung 950, Taiwan
| | - Jiunn-Wang Liao
- Graduate Institute of Veterinary Pathobiology, National Chung Hsing University, Taichung 402, Taiwan
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25
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Hui CY, Hu SY, Yang XQ, Guo Y. A panel of visual bacterial biosensors for the rapid detection of genotoxic and oxidative damage: A proof of concept study. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 888:503639. [PMID: 37188434 DOI: 10.1016/j.mrgentox.2023.503639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
The emergence of new compounds during the past decade requires a high-throughput screening method for toxicity assay. The stress-responsive whole-cell biosensor is a powerful tool to evaluate direct or indirect damages of biological macromolecules induced by toxic chemicals. In this proof-of-concept study, nine well-characterized stress-responsive promoters were first selected to assemble a set of blue indigoidine-based biosensors. The PuspA-based, PfabA-based, and PgrpE-based biosensors were eliminated due to their high background. A dose-dependent increase of visible blue signal was observed in PrecA-, PkatG-, and PuvrA-based biosensors, responsive to potent mutagens, including mitomycin and nalidixic acid, but not to genotoxic lead and cadmium. The PrecA, PkatG, and Ppgi gene promoters were further fused to a purple deoxyviolacein synthetic enzyme cluster. Although high basal production of deoxyviolacein is unavoidable, an enhanced visible purple signal in response to mitomycin and nalidixic acid was observed as dose-dependent, especially in PkatG-based biosensors. The study shows that a set of stress-responsive biosensors employing visible pigment as a reporter is pre-validating in detecting extensive DNA damage and intense oxidative stress. Unlike widely-used fluorescent and bioluminescent biosensors, the visual pigment-based biosensor can become a novel, low-cost, mini-equipment, and high-throughput colorimetric device for the toxicity assessment of chemicals. However, combining multiple improvements can further improve the biosensing performance in future studies.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Shun-Yu Hu
- Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xue-Qin Yang
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
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26
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Lou C, Yang H, Deng H, Huang M, Li W, Liu G, Lee PW, Tang Y. Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods. J Cheminform 2023; 15:35. [PMID: 36941726 PMCID: PMC10029263 DOI: 10.1186/s13321-023-00707-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Chemical mutagenicity is a serious issue that needs to be addressed in early drug discovery. Over a long period of time, medicinal chemists have manually summarized a series of empirical rules for the optimization of chemical mutagenicity. However, given the rising amount of data, it is getting more difficult for medicinal chemists to identify more comprehensive chemical rules behind the biochemical data. Herein, we integrated a large Ames mutagenicity data set with 8576 compounds to derive mutagenicity transformation rules for reversing Ames mutagenicity via matched molecular pairs analysis. A well-trained consensus model with a reasonable applicability domain was constructed, which showed favorable performance in the external validation set with an accuracy of 0.815. The model was used to assess the generalizability and validity of these mutagenicity transformation rules. The results demonstrated that these rules were of great value and could provide inspiration for the structural modifications of compounds with potential mutagenic effects. We also found that the local chemical environment of the attachment points of rules was critical for successful transformation. To facilitate the use of these mutagenicity transformation rules, we integrated them into ADMETopt2 ( http://lmmd.ecust.edu.cn/admetsar2/admetopt2/ ), a free web server for optimization of chemical ADMET properties. The above-mentioned approach would be extended to the optimization of other toxicity endpoints.
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Affiliation(s)
- Chaofeng Lou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Hongbin Yang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Hua Deng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Mengting Huang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Philip W Lee
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
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27
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Schietgat L, Cuissart B, De Grave K, Efthymiadis K, Bureau R, Crémilleux B, Ramon J, Lepailleur A. Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm. Mol Inform 2023; 42:e2200232. [PMID: 36529710 DOI: 10.1002/minf.202200232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/23/2022]
Abstract
Maximum common substructures (MCS) have received a lot of attention in the chemoinformatics community. They are typically used as a similarity measure between molecules, showing high predictive performance when used in classification tasks, while being easily explainable substructures. In the present work, we applied the Pairwise Maximum Common Subgraph Feature Generation (PMCSFG) algorithm to automatically detect toxicophores (structural alerts) and to compute fingerprints based on MCS. We present a comparison between our MCS-based fingerprints and 12 well-known chemical fingerprints when used as features in machine learning models. We provide an experimental evaluation and discuss the usefulness of the different methods on mutagenicity data. The features generated by the MCS method have a state-of-the-art performance when predicting mutagenicity, while they are more interpretable than the traditional chemical fingerprints.
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Affiliation(s)
- Leander Schietgat
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussel, Belgium.,Department of Computer Science, KU Leuven, Leuven, Belgium
| | - Bertrand Cuissart
- Groupe de Recherche en Informatique, Image, Automatique et Instrumentation de Caen, UNICAEN, ENSICAEN, CNRS - UMR GREYC, Normandie Univ., Caen, France
| | | | | | - Ronan Bureau
- Centre d'Etudes et de Recherche sur le Médicament de Normandie, UNICAEN, CERMN, Normandie Univ., Caen, France
| | - Bruno Crémilleux
- Groupe de Recherche en Informatique, Image, Automatique et Instrumentation de Caen, UNICAEN, ENSICAEN, CNRS - UMR GREYC, Normandie Univ., Caen, France
| | - Jan Ramon
- INRIA Lille Nord Europe, Lille, France
| | - Alban Lepailleur
- Centre d'Etudes et de Recherche sur le Médicament de Normandie, UNICAEN, CERMN, Normandie Univ., Caen, France
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28
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Cheohen CFDAR, Esteves MEA, da Fonseca TS, Leal CM, Assis FDLF, Campos MF, Rebelo RS, Allonso D, Leitão GG, da Silva ML, Leitão SG. In silico screening of phenylethanoid glycosides, a class of pharmacologically active compounds as natural inhibitors of SARS-CoV-2 proteases. Comput Struct Biotechnol J 2023; 21:1461-1472. [PMID: 36817956 PMCID: PMC9920770 DOI: 10.1016/j.csbj.2023.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023] Open
Abstract
Since the advent of Covid-19, several natural products have been investigated regarding their in silico interactions with SARS-CoV-2 proteases - 3CLpro and PLpro, two of the most important pharmacological targets for antiviral development. Phenylethanoid glycosides (PG) are a class of natural products present in important medicinal plants and a drug containing this group of active ingredients has been successfully used in the treatment of Covid-19 in China. Thus, a dataset with 567 derivatives of this class was built from reviews published between 1994 and 2020, and their interaction against both SARS-CoV-2 proteases was investigated. The virtual screening was performed by filtering the PGs through the evaluation of scores based on the AutoDock Vina, GOLD/ChemPLP, and GOLD/GoldScore evaluation functions. The bRO5 pharmacokinetic parameters of the PGs ranked in the previous step were analyzed and their interaction with key amino acid residues of the 3CLpro and PLpro enzymes was evaluated. Ninety-eight compounds were identified by computational approaches against PLpro and 80 PGs against 3CLpro. Of these, four interacted with key catalytic residues of PLpro, which is an indicative of inhibitory activity, and three compounds interacted with catalytic key residues of 3CLpro. Of these, five PGs occur in plants of the Traditional Chinese Medicine (TCM), while two are components of plants/formulations currently used in the Covid-19 protocols in China. The data presented here show the potential of PGs as selective inhibitors of SARS-CoV-2 3CLpro and PLpro.
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Affiliation(s)
- Caio Felipe de Araujo Ribas Cheohen
- Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965045, Brazil
| | - Maria Eduarda Alves Esteves
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, RJ 21041361, Brazil
| | - Thamirys Silva da Fonseca
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Carla Monteiro Leal
- Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Fernanda de Lemos Fernandes Assis
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Mariana Freire Campos
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Raianne Soares Rebelo
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Diego Allonso
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil
| | - Manuela Leal da Silva
- Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965045, Brazil,Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, RJ 21041361, Brazil,Corresponding author at: Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965045, Brazil.
| | - Suzana Guimarães Leitão
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil,Corresponding author at: Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941902, Brazil.
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Large DN, Van Doorn NA, Timmons SC. Cancer and chemicals: A research-inspired laboratory exercise based on the Ames test for mutagenicity. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:103-113. [PMID: 36098335 DOI: 10.1002/bmb.21674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 05/26/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Laboratory courses should cultivate enthusiasm for research and an appreciation for real-world scientific challenges to retain undergraduate students and encourage them to pursue STEM-related careers. Course-based undergraduate research experiences (CURE) have emerged as an inclusive pedagogical model that facilitates laboratory skill development, while also improving self-efficacy and critical thinking skills. Herein, an innovative research-inspired Ames test for mutagenicity project is described. Students choose their own project theme and investigate substances using both TA98 and TA100 strains of Salmonella typhimurium to evaluate the potential for frameshift mutations and base-pair substitutions, respectively. An appropriate test concentration of each substance is first determined via a cytotoxicity assay, providing an additional learning opportunity. Students also study the mutagenicity of test substance metabolites using commercially available rat liver extracts to simulate metabolism. Overall, these experiences provide a comprehensive research project with high relevancy to human health and real-world importance. This laboratory module was assessed using CURE pre- and post-course surveys to evaluate learning gains and benefits. Assessment data illustrated that students appreciated the discovery aspect of the research project and gained skills related to reading scientific literature and effective poster presentations. Student-reported benefits of research project participation included learning new laboratory techniques, enhanced scientific writing skills, an increased tolerance for and understanding of common research challenges, and the confidence to tackle more complex research endeavors. Narrative feedback from students was very positive, with project highlights being the opportunity to select their own test substances and create new knowledge, as well as the analysis of results.
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Affiliation(s)
- Delaney N Large
- Department of Natural Sciences, Lawrence Technological University, Southfield, Michigan, USA
| | - Nathaniel A Van Doorn
- Department of Natural Sciences, Lawrence Technological University, Southfield, Michigan, USA
| | - Shannon C Timmons
- Department of Natural Sciences, Lawrence Technological University, Southfield, Michigan, USA
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30
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Stojanowska A, Zeynalli F, Wróbel M, Rybak J. The use of spider webs in the monitoring of air quality-A review. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2023; 19:32-44. [PMID: 35304975 DOI: 10.1002/ieam.4607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/31/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Methods for using spider webs as passive air samplers have been developed over recent years and reported in more than a dozen articles. In this article, we present the typical procedures followed when using this new tool and critically review its application in air pollution assessment. To understand the state of research and application of spider webs in this field, we describe some advantages and disadvantages of their use in the analyses of air contaminants. The aim is to summarize the current knowledge on this subject, highlight gaps in the present studies, and arouse the interest of scientists on this issue. The increased effort could result in the standardization of the method at the national and international level. Integr Environ Assess Manag 2023;19:32-44. © 2022 SETAC.
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Affiliation(s)
- Agnieszka Stojanowska
- Faculty of Environmental Engineering, Wrocław University of Science and Technology, Wrocław, Poland
| | - Farhad Zeynalli
- Faculty of Environmental Engineering, Wrocław University of Science and Technology, Wrocław, Poland
| | - Magdalena Wróbel
- Faculty of Environmental Engineering, Wrocław University of Science and Technology, Wrocław, Poland
| | - Justyna Rybak
- Faculty of Environmental Engineering, Wrocław University of Science and Technology, Wrocław, Poland
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Abstract
Leishmaniasis (visceral and cutaneous), Chagas disease and human African trypanosomiasis cause substantial death and morbidity, particularly in low- and middle-income countries. Although the situation has improved for human African trypanosomiasis, there remains an urgent need for new medicines to treat leishmaniasis and Chagas disease; the clinical development pipeline is particularly sparse for Chagas disease. In this Review, we describe recent advances in our understanding of the biology of the causative pathogens, particularly from the drug discovery perspective, and we explore the progress that has been made in the development of new drug candidates and the identification of promising molecular targets. We also explore the challenges in developing new clinical candidates and discuss potential solutions to overcome such hurdles.
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32
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Martínez MJ, Sabando MV, Soto AJ, Roca C, Requena-Triguero C, Campillo NE, Páez JA, Ponzoni I. Multitask Deep Neural Networks for Ames Mutagenicity Prediction. J Chem Inf Model 2022; 62:6342-6351. [PMID: 36066065 DOI: 10.1021/acs.jcim.2c00532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Ames mutagenicity test constitutes the most frequently used assay to estimate the mutagenic potential of drug candidates. While this test employs experimental results using various strains of Salmonella typhimurium, the vast majority of the published in silico models for predicting mutagenicity do not take into account the test results of the individual experiments conducted for each strain. Instead, such QSAR models are generally trained employing overall labels (i.e., mutagenic and nonmutagenic). Recently, neural-based models combined with multitask learning strategies have yielded interesting results in different domains, given their capabilities to model multitarget functions. In this scenario, we propose a novel neural-based QSAR model to predict mutagenicity that leverages experimental results from different strains involved in the Ames test by means of a multitask learning approach. To the best of our knowledge, the modeling strategy hereby proposed has not been applied to model Ames mutagenicity previously. The results yielded by our model surpass those obtained by single-task modeling strategies, such as models that predict the overall Ames label or ensemble models built from individual strains. For reproducibility and accessibility purposes, all source code and datasets used in our experiments are publicly available.
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Affiliation(s)
- María Jimena Martínez
- ISISTAN (CONICET - UNCPBA) Campus Universitario - Paraje Arroyo Seco, 7000, Tandil, Argentina
| | - María Virginia Sabando
- Institute for Computer Science and Engineering, UNS-CONICET, 8000, Bahía Blanca, Argentina.,Department of Computer Science and Engineering, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
| | - Axel J Soto
- Institute for Computer Science and Engineering, UNS-CONICET, 8000, Bahía Blanca, Argentina.,Department of Computer Science and Engineering, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
| | - Carlos Roca
- CIB Margarita Salas (CSIC) Ramiro de Maeztu, 9. 28740, Madrid, Spain
| | | | - Nuria E Campillo
- CIB Margarita Salas (CSIC) Ramiro de Maeztu, 9. 28740, Madrid, Spain.,Instituto de Ciencias Matemáticas (CSIC), Nicolás Cabrera, no13-15, Campus de Cantoblanco, UAM, CP 28049, Madrid, Spain
| | - Juan A Páez
- Instituto de Química Médica. Consejo Superior de Investigaciones Científicas (CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Ignacio Ponzoni
- Institute for Computer Science and Engineering, UNS-CONICET, 8000, Bahía Blanca, Argentina.,Department of Computer Science and Engineering, Universidad Nacional del Sur, 8000, Bahía Blanca, Argentina
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33
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Barros B, Oliveira M, Morais S. Unveiling Urinary Mutagenicity by the Ames Test for Occupational Risk Assessment: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13074. [PMID: 36293654 PMCID: PMC9603210 DOI: 10.3390/ijerph192013074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Occupational exposure may involve a variety of toxic compounds. A mutagenicity analysis using the Ames test can provide valuable information regarding the toxicity of absorbed xenobiotics. Through a search of relevant databases, this systematic review gathers and critically discusses the published papers (excluding other types of publications) from 2001-2021 that have assessed urinary mutagenicity (Ames test with Salmonella typhimurium) in an occupational exposure context. Due to the heterogeneity of the study methods, a meta-analysis could not be conducted. The characterized occupations were firefighters, traffic policemen, bus drivers, mail carriers, coke oven and charcoal workers, chemical laboratory staff, farmers, pharmacy workers, and professionals from several other industrial sectors. The genetically modified bacterial strains (histidine dependent) TA98, TA100, YG1041, YG1021, YG1024 and YG1042 have been used for the health risk assessment of individual (e.g., polycyclic aromatic hydrocarbons) and mixtures of compounds (e.g., diesel engine exhaust, fire smoke, industrial fumes/dyes) in different contexts. Although comparison of the data between studies is challenging, urinary mutagenicity can be very informative of possible associations between work-related exposure and the respective mutagenic potential. Careful interpretation of results and their direct use for occupational health risk assessment are crucial and yet complex; the use of several strains is highly recommended since individual and/or synergistic effects of complex exposure to xenobiotics can be overlooked. Future studies should improve the methods used to reach a standardized protocol for specific occupational environments to strengthen the applicability of the urinary mutagenicity assay and reduce inter- and intra-individual variability and exposure source confounders.
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34
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Darbandi A, Mirkalantari S, Golmoradi Zadeh R, Esghaei M, Talebi M, Kakanj M. Safety evaluation of mutagenicity, genotoxicity, and cytotoxicity of Lactobacillus spp. isolates as probiotic candidates. J Clin Lab Anal 2022; 36:e24481. [PMID: 35582746 PMCID: PMC9279957 DOI: 10.1002/jcla.24481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/15/2022] [Accepted: 04/23/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Probiotics promote a healthy balance of gut bacteria and have many beneficial effects on human digestive physiology. Although, few side effects of probiotics have been reported. This study aimed to assess the safety of five probiotic candidate Lactobacillus strains isolated from healthy individuals by examining mutagenicity, genotoxicity, and oral toxic effects. METHODS Five selected candidate probiotic (SCPs) strains were evaluated for genotoxicity (Ames test with Salmonella typhimurium), in vitro mammalian chromosome aberration test and an in vivo mouse micronucleus assay on peripheral blood of mice. To evaluate the oral dose toxicity, BALB/c mice models were treated repeatedly (2000, 1000, and 500 mg/kg body weight /day) for 28-days. RESULTS The Ames test performed for two S. typhimurium strains TA 98 and TA100 (both in the absence and in the presence of S-9 metabolic activation system) did not show an increase in reverse mutation because of exposure to the SCPs in any of the doses (5.0, 2.5, 1.25, 0.625, and 0.3125 mg/plate). There was no genotoxicity in the SCPs treatment in the vitro chromosome aberration assay with Chinese hamster ovary cells (CHO-K1). In addition, none of the tested strains increased the frequency of micronucleated reticulocytes in reticulocytes, the SCPs with the studied doses caused no substantial variation in the experimental groups compared to the negative control group (p > 0.05). SCPs were not acutely toxic when administered to male and female BALB/c mice by single gavage at (2000, 1000, and 500 mg/kg b.w/day) with no mortality or clinical signs, change in body weight or macroscopic abnormalities were observed in this dose range. CONCLUSION As a result, SCPs did not induce mutagenic potential in vitro with bacterial reverse mutation, clastogenicity, and in vivo tests in the ranges of concentrations evaluated in our study.
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Affiliation(s)
- Atieh Darbandi
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shiva Mirkalantari
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rezvan Golmoradi Zadeh
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Esghaei
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Kakanj
- Food and Drug Laboratory Research Center, Food and Drug Administration, MOH&ME, Tehran, Iran
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35
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The interplay between anticancer challenges and the microbial communities from the gut. Eur J Clin Microbiol Infect Dis 2022; 41:691-711. [PMID: 35353280 DOI: 10.1007/s10096-022-04435-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/15/2022] [Indexed: 11/03/2022]
Abstract
Cancer being an increasing burden on human health, the use of anticancer drugs has risen over the last decades. The physiological effects of these drugs are not only perceived by the host's cells but also by the microbial cells it harbors as commensals, notably the gut microbiota. Since the early '50 s, the cytotoxicity of anticancer chemotherapy was evaluated on bacteria revealing some antimicrobial activities that result in an established perturbation of the gut microbiota. This perturbation can affect the host's health through dysbiosis, which can lead to multiple complications, but has also been shown to have a direct effect on the treatment efficiency.We, therefore, conducted a review of literature focusing on this triangular relationship involving the microbial communities from the gut, the host's disease, and the anticancer treatment. We focused specifically on the antimicrobial effects of anticancer chemotherapy, their impact on mutagenesis in bacteria, and the perspectives of using bacteria-based tools to help in the diagnostic and treatment of cancer.
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36
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Lin YE, Lin MH, Yeh TY, Lai YS, Lu KH, Huang HS, Peng FC, Liu SH, Sheen LY. Genotoxicity and 28-day repeated dose oral toxicity study of garlic essential oil in mice. J Tradit Complement Med 2022; 12:536-544. [DOI: 10.1016/j.jtcme.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/18/2022] [Accepted: 05/01/2022] [Indexed: 11/28/2022] Open
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37
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Kullmann A, Kridner D, Mertens S, Christianson M, Rosa D, Diaz-Botia CA. First Food and Drug Administration Cleared Thin-Film Electrode for Intracranial Stimulation, Recording, and Monitoring of Brain Activity—Part 1: Biocompatibility Testing. Front Neurosci 2022; 16:876877. [PMID: 35573282 PMCID: PMC9100917 DOI: 10.3389/fnins.2022.876877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Subdural strip and grid invasive electroencephalography electrodes are routinely used for surgical evaluation of patients with drug-resistant epilepsy (DRE). Although these electrodes have been in the United States market for decades (first FDA clearance 1985), their fabrication, materials, and properties have hardly changed. Existing commercially available electrodes are made of silicone, are thick (>0.5 mm), and do not optimally conform to brain convolutions. New thin-film polyimide electrodes (0.08 mm) have been manufactured to address these issues. While different thin-film electrodes are available for research use, to date, only one electrode is cleared by Food and Drug Administration (FDA) for use in clinical practice. This study describes the biocompatibility tests that led to this clearance. Biocompatibility was tested using standard methods according to International Organization for Standardization (ISO) 10993. Electrodes and appropriate control materials were bent, folded, and placed in the appropriate extraction vehicles, or implanted. The extracts were used for in vitro and in vivo tests, to assess the effects of any potential extractable and leachable materials that may be toxic to the body. In vitro studies included cytotoxicity tested in L929 cell line, genotoxicity tested using mouse lymphoma assay (MLA) and Ames assay, and hemolysis tested in rabbit whole blood samples. The results indicated that the electrodes were non-cytotoxic, non-mutagenic, non-clastogenic, and non-hemolytic. In vivo studies included sensitization tested in guinea pigs, irritation tested in rabbits, acute systemic toxicity testing in mice, pyrogenicity tested in rabbits, and a prolonged 28-day subdural implant in sheep. The results indicated that the electrodes induced no sensitization and irritation, no weight loss, and no temperature increase. Histological examination of the sheep brain tissue showed no or minimal immune cell accumulation, necrosis, neovascularization, fibrosis, and astrocyte infiltration, with no differences from the control material. In summary, biocompatibility studies indicated that these new thin-film electrodes are appropriate for human use. As a result, the electrodes were cleared by the FDA for use in clinical practice [510(k) K192764], making it the first thin-film subdural electrode to progress from research to clinic. Its readiness as a commercial product ensures availability to all patients undergoing surgical evaluation for DRE.
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38
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Tang ML, Li H, Ning JF, Shen X, Sun X. Discovery of First-in-Class TAK1-MKK3 Protein-Protein Interaction (PPI) Inhibitor (R)-STU104 for the Treatment of Ulcerative Colitis through Modulating TNF-α Production. J Med Chem 2022; 65:6690-6709. [PMID: 35442672 DOI: 10.1021/acs.jmedchem.1c02198] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tumor necrosis factor α (TNF-α) has been demonstrated to be a therapeutic target for autoimmune diseases. However, this biological therapy exhibits some inevitable disadvantages, such as risk of infection. Thus, small-molecule alternatives by targeting TNF-α production signaling pathway are still in demand. Herein, we describe the design, synthesis, and structure-activity relationships of 3-aryindanone compounds regarding their modulation of TNF-α production. Among them, (R)-STU104 exhibited the most potent inhibitory activity on TNF-α production, which suppressed the TAK1/MKK3/p38/MnK1/MK2/elF4E signal pathways through binding with MKK3 and disrupting the TAK1 phosphorylating MKK3. As a result, (R)-STU104 demonstrated remarkable dose-effect relationships on both acute and chronic mouse UC models. In addition to its good pharmacokinetic (PK) and safety profile, (R)-STU104 showed better anti-UC efficacy in vivo at 10 mg/kg/d than mesalazine at the dose of 50 mg/kg/d. These results suggested that TAK1-MKK3 interaction inhibitors could be potentially utilized for the treatment of UC.
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Affiliation(s)
- Mei-Lin Tang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Haidong Li
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jin-Feng Ning
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Xiaoyan Shen
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Xun Sun
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,The Institutes of Integrative Medicine of Fudan University, 12 Wulumuqi Zhong Road, Shanghai 200040, China
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39
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Smith A, Wall RJ, Patterson S, Rowan T, Rico Vidal E, Stojanovski L, Huggett M, Hampton SE, Thomas MG, Corpas Lopez V, Gillingwater K, Duke J, Napier G, Peter R, Vitouley HS, Harrison JR, Milne R, Jeacock L, Baker N, Davis SH, Simeons F, Riley J, Horn D, Brun R, Zuccotto F, Witty MJ, Wyllie S, Read KD, Gilbert IH. Repositioning of a Diaminothiazole Series Confirmed to Target the Cyclin-Dependent Kinase CRK12 for Use in the Treatment of African Animal Trypanosomiasis. J Med Chem 2022; 65:5606-5624. [PMID: 35303411 PMCID: PMC9014415 DOI: 10.1021/acs.jmedchem.1c02104] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 11/29/2022]
Abstract
African animal trypanosomiasis or nagana, caused principally by infection of the protozoan parasites Trypanosoma congolense and Trypanosoma vivax, is a major problem in cattle and other livestocks in sub-Saharan Africa. Current treatments are threatened by the emergence of drug resistance and there is an urgent need for new, effective drugs. Here, we report the repositioning of a compound series initially developed for the treatment of human African trypanosomiasis. A medicinal chemistry program, focused on deriving more soluble analogues, led to development of a lead compound capable of curing cattle infected with both T. congolense and T. vivax via intravenous dosing. Further optimization has the potential to yield a single-dose intramuscular treatment for this disease. Comprehensive mode of action studies revealed that the molecular target of this promising compound and related analogues is the cyclin-dependent kinase CRK12.
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Affiliation(s)
- Alasdair Smith
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Richard J. Wall
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Stephen Patterson
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Tim Rowan
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Eva Rico Vidal
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Laste Stojanovski
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Margaret Huggett
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Shahienaz E. Hampton
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Michael G. Thomas
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Victoriano Corpas Lopez
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Kirsten Gillingwater
- Swiss
Tropical and Public Health Institute, Socinstrasse 57, CH-4002 Basel, Switzerland
- University
of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Jeff Duke
- University
of Greenwich, Medway Campus, Central Avenue, Chatham Maritime, Chatham, Kent ME4 4TB United Kingdom
| | - Grant Napier
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Rose Peter
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Hervé S. Vitouley
- Centre
International de Recherche-Développement sur l’Elevage
en zone Subhumide (CIRDES), No 559 ru
5-31 angle Av. du Gouverneur Louveau, 01 BP: 454 Bobo-Dioulasso 01, Burkina Faso
| | - Justin R. Harrison
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Rachel Milne
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Laura Jeacock
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Nicola Baker
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Susan H. Davis
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Frederick Simeons
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Jennifer Riley
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - David Horn
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Reto Brun
- Swiss
Tropical and Public Health Institute, Socinstrasse 57, CH-4002 Basel, Switzerland
- University
of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Fabio Zuccotto
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Michael J Witty
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Susan Wyllie
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Kevin D. Read
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Ian H. Gilbert
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
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Maslov AY, Makhortov S, Sun S, Heid J, Dong X, Lee M, Vijg J. Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing. SCIENCE ADVANCES 2022; 8:eabm3259. [PMID: 35394831 PMCID: PMC8993124 DOI: 10.1126/sciadv.abm3259] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Postzygotic somatic mutations have been found associated with human disease, including diseases other than cancer. Most information on somatic mutations has come from studying clonally amplified mutant cells, based on a growth advantage or genetic drift. However, almost all somatic mutations are unique for each cell, and the quantitative analysis of these low-abundance mutations in normal tissues remains a major challenge in biology. Here, we introduce single-molecule mutation sequencing (SMM-seq), a novel approach for quantitative identification of point mutations in normal cells and tissues.
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Affiliation(s)
- Alexander Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Sergey Makhortov
- Department of Programming and Information Technology, Voronezh State University, Voronezh, Russia
| | - Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Johanna Heid
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute on the Biology of Aging and Metabolism and Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Kandsi F, Elbouzidi A, Lafdil FZ, Meskali N, Azghar A, Addi M, Hano C, Maleb A, Gseyra N. Antibacterial and Antioxidant Activity of Dysphania ambrosioides (L.) Mosyakin and Clemants Essential Oils: Experimental and Computational Approaches. Antibiotics (Basel) 2022; 11:482. [PMID: 35453233 PMCID: PMC9031865 DOI: 10.3390/antibiotics11040482] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 02/06/2023] Open
Abstract
Dysphania ambrosioides (L.) Mosyakin and Clemants, also known as Mexican tea, and locally known as Mkhinza, is a polymorphic annual and perennial herb, and it is widely used in folk medicine to treat a broad range of illnesses in Morocco. The aim of this study was to determine the phytochemical content and the antioxidant and the antibacterial properties of essential oils isolated from D. ambrosioides aerial components, growing in Eastern Morocco (Figuig). Hydrodistillation was used to separate D. ambrosioides essential oils, and the abundance of each phytocompound was determined by using Gas Chromatography coupled with Mass Spectrometry (GC-MS). In vitro 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and inhibition of β-carotene/linoleic acid bleaching assays were used to determine D. ambrosioides essential oils' antioxidant activity. The findings revealed relative antioxidative power and modest radical scavenging. The antibacterial activity of the essential oils was broad-spectrum, with Escherichia coli, Staphylococcus aureus, and Enterococcus faecalis as the most susceptible strains tested. To elucidate the physicochemical nature, drug-likeness, and the antioxidant and antibacterial action of the identified phytocomponents, computational techniques, such as ADMET analysis, and molecular docking were used.
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Affiliation(s)
- Fahd Kandsi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco; (F.K.); (F.Z.L.); (N.G.)
| | - Amine Elbouzidi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco; (A.E.); (N.M.)
| | - Fatima Zahra Lafdil
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco; (F.K.); (F.Z.L.); (N.G.)
| | - Nada Meskali
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco; (A.E.); (N.M.)
| | - Ali Azghar
- Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU), Oujda 60000, Morocco; (A.A.); (A.M.)
| | - Mohamed Addi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco; (A.E.); (N.M.)
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, University of Orleans, CEDEX 2, 45067 Orléans, France
- Le StudiumInstitue for Advanced Studies, 1 Rue Dupanloup, 45000 Orléans, France
| | - Adil Maleb
- Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU), Oujda 60000, Morocco; (A.A.); (A.M.)
| | - Nadia Gseyra
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco; (F.K.); (F.Z.L.); (N.G.)
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42
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Johann S, Weichert FG, Schröer L, Stratemann L, Kämpfer C, Seiler TB, Heger S, Töpel A, Sassmann T, Pich A, Jakob F, Schwaneberg U, Stoffels P, Philipp M, Terfrüchte M, Loeschcke A, Schipper K, Feldbrügge M, Ihling N, Büchs J, Bator I, Tiso T, Blank LM, Roß-Nickoll M, Hollert H. A plea for the integration of Green Toxicology in sustainable bioeconomy strategies - Biosurfactants and microgel-based pesticide release systems as examples. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:127800. [PMID: 34865895 DOI: 10.1016/j.jhazmat.2021.127800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/30/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
A key aspect of the transformation of the economic sector towards a sustainable bioeconomy is the development of environmentally friendly alternatives for hitherto used chemicals, which have negative impacts on environmental health. However, the implementation of an ecotoxicological hazard assessment at early steps of product development to elaborate the most promising candidates of lowest harm is scarce in industry practice. The present article introduces the interdisciplinary proof-of-concept project GreenToxiConomy, which shows the successful application of a Green Toxicology strategy for biosurfactants and a novel microgel-based pesticide release system. Both groups are promising candidates for industrial and agricultural applications and the ecotoxicological characterization is yet missing important information. An iterative substance- and application-oriented bioassay battery for acute and mechanism-specific toxicity within aquatic and terrestrial model species is introduced for both potentially hazardous materials getting into contact with humans and ending up in the environment. By applying in silico QSAR-based models on genotoxicity, endocrine disruption, skin sensitization and acute toxicity to algae, daphnids and fish, individual biosurfactants resulted in deviating toxicity, suggesting a pre-ranking of the compounds. Experimental toxicity assessment will further complement the predicted toxicity to elaborate the most promising candidates in an efficient pre-screening of new substances.
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Affiliation(s)
- Sarah Johann
- Department Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany.
| | - Fabian G Weichert
- Department Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany; Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lukas Schröer
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lucas Stratemann
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Christoph Kämpfer
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Thomas-Benjamin Seiler
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; Hygiene-Institut des Ruhrgebiets, Rotthauser Str. 21, 45879 Gelsenkirchen, Germany
| | - Sebastian Heger
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Alexander Töpel
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1-2, 52074 Aachen, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Tim Sassmann
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1-2, 52074 Aachen, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Andrij Pich
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1-2, 52074 Aachen, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany; Aachen Maastricht Institute for Biobased Materials, Maastricht University, Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Felix Jakob
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52074 Aachen, Germany; Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Peter Stoffels
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute for Microbiology, Department Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Magnus Philipp
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute for Microbiology, Department Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Marius Terfrüchte
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute for Microbiology, Department Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Anita Loeschcke
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, 52425 Jülich, Germany
| | - Kerstin Schipper
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute for Microbiology, Department Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Michael Feldbrügge
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute for Microbiology, Department Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Nina Ihling
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074 Aachen, Germany
| | - Jochen Büchs
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074 Aachen, Germany
| | - Isabel Bator
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Till Tiso
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lars M Blank
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany; Institute of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Martina Roß-Nickoll
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Henner Hollert
- Department Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany; Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany.
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Galati S, Di Stefano M, Martinelli E, Macchia M, Martinelli A, Poli G, Tuccinardi T. VenomPred: A Machine Learning Based Platform for Molecular Toxicity Predictions. Int J Mol Sci 2022; 23:ijms23042105. [PMID: 35216217 PMCID: PMC8877213 DOI: 10.3390/ijms23042105] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 12/28/2022] Open
Abstract
The use of in silico toxicity prediction methods plays an important role in the selection of lead compounds and in ADMET studies since in vitro and in vivo methods are often limited by ethics, time, budget and other resources. In this context, we present our new web tool VenomPred, a user-friendly platform for evaluating the potential mutagenic, hepatotoxic, carcinogenic and estrogenic effects of small molecules. VenomPred platform employs several in-house Machine Learning (ML) models developed with datasets derived from VEGA QSAR, a software that includes a comprehensive collection of different toxicity models and has been used as a reference for building and evaluating our ML models. The results showed that our models achieved equal or better performance than those obtained with the reference models included in VEGA QSAR. In order to improve the predictive performance of our platform, we adopted a consensus approach combining the results of different ML models, which was able to predict chemical toxicity better than the single models. This improved method was thus implemented in the VenomPred platform, a freely accessible webserver that takes the SMILES (Simplified Molecular-Input Line-Entry System) strings of the compounds as input and sends the prediction results providing a probability score about their potential toxicity.
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Affiliation(s)
- Salvatore Galati
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (E.M.); (M.M.); (A.M.); (T.T.)
| | - Miriana Di Stefano
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (E.M.); (M.M.); (A.M.); (T.T.)
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Elisa Martinelli
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (E.M.); (M.M.); (A.M.); (T.T.)
| | - Marco Macchia
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (E.M.); (M.M.); (A.M.); (T.T.)
| | - Adriano Martinelli
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (E.M.); (M.M.); (A.M.); (T.T.)
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (E.M.); (M.M.); (A.M.); (T.T.)
- Correspondence: ; Tel.: +39-050-2219603
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (S.G.); (M.D.S.); (E.M.); (M.M.); (A.M.); (T.T.)
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Pharmaceutical and Safety Profile Evaluation of Novel Selenocompounds with Noteworthy Anticancer Activity. Pharmaceutics 2022; 14:pharmaceutics14020367. [PMID: 35214099 PMCID: PMC8875489 DOI: 10.3390/pharmaceutics14020367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Prior studies have reported the potent and selective cytotoxic, pro-apoptotic, and chemopreventive activities of a cyclic selenoanhydride and of a series of selenoesters. Some of these selenium derivatives demonstrated multidrug resistance (MDR)-reversing activity in different resistant cancer cell lines. Thus, the aim of this study was to evaluate the pharmaceutical and safety profiles of these selected selenocompounds using alternative methods in silico and in vitro. One of the main tasks of this work was to determine both the physicochemical properties and metabolic stability of these selenoesters. The obtained results proved that these tested selenocompounds could become potential candidates for novel and safe anticancer drugs with good ADMET parameters. The most favorable selenocompounds turned out to be the phthalic selenoanhydride (EDA-A6), two ketone-containing selenoesters with a 4-chlorophenyl moiety (EDA-71 and EDA-73), and a symmetrical selenodiester with a pyridine ring and two selenium atoms (EDA-119).
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45
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Maliwal D, Pissurlenkar RRS, Telvekar V. Identification of Novel Potential Anti-Diabetic Candidates targeting Human Pancreatic ɑ-Amylase and Human ɑ-Glycosidase: An Exhaustive Structure-based Screening. CAN J CHEM 2021. [DOI: 10.1139/cjc-2021-0238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diabetes is a major health issue that half a billion people affected worldwide. It is a serious, long-term medical condition majorly impacting the lives and well-being of individuals, families, and societies at large. It is amongst the top 10 diseases responsible for the death amongst adults with an expected rise to 10.2% (578 million) by 2030 and 10.9% (700 million) by 2045. The carbohydrates absorbed into the body are hydrolyzed by pancreatic α-amylase and other enzymes, human α-glucosidase. The α-amylase and α-glucosidase are validated therapeutic targets in the treatment of Type II diabetes (T2DM) as they play a vital role in modulating the blood glucose post meal. Herein, we report novel and diverse molecules as potential candidates, with predicted affinity for α-amylase and α-glucosidase. These molecules have been identified via hierarchical multistep docking of small molecules database with the estimated binding free energies. A Glide XP Score cutoff −8.00 kcal/mol was implemented to filter out non potential molecules. Four molecules viz. amb22034702, amb18105639, amb17153304, and amb9760832 have been identified after an exhaustive computational study involving, evaluation of binding interactions and assessment of the pharmacokinetics and toxicity profiles. The in-depth analysis of protein– ligand interactions was performed using a 100ns molecular dynamics (MD) simulation to establish the dynamic stability. Furthermore MM-GBSA based binding free energies were computed for 1000 trajectory snapshots to ascertain the strong binding affinity of these molecules for α-amylase and αglucosidase. The identified molecules can be considered as promising candidates for further drug development through necessary experimental assessments.
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Affiliation(s)
- Deepika Maliwal
- Institute of Chemical Technology, 52735, Department of Pharmaceutical Sciences and Technology, Mumbai, Maharashtra, India
| | | | - Vikas Telvekar
- Institute of Chemical Technology, 52735, Department of Pharmaceutical Sciences and Technology, Mumbai, Maharashtra, India
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46
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Sleight TW, Sexton CN, Mpourmpakis G, Gilbertson LM, Ng CA. A Classification Model to Identify Direct-Acting Mutagenic Polycyclic Aromatic Hydrocarbon Transformation Products. Chem Res Toxicol 2021; 34:2273-2286. [PMID: 34662518 DOI: 10.1021/acs.chemrestox.1c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a complex group of environmental contaminants, many having long environmental half-lives. As these compounds degrade, the changes in their structure can result in a substantial increase in mutagenicity compared to the parent compound. Over time, each individual PAH can potentially degrade into several thousand unique transformation products, creating a complex, constantly evolving set of intermediates. Microbial degradation is the primary mechanism of their transformation and ultimate removal from the environment, and this process can result in mutagenic activation similar to the metabolic activation that can occur in multicellular organisms. The diversity of the potential intermediate structures in PAH-contaminated environments renders hazard assessment difficult for both remediation professionals and regulators. A mixture of structural and energetic descriptors has proven effective in existing studies for classifying which PAH transformation products will be mutagenic. However, most existing studies of environmental PAH mutagens primarily focus on nitrogenated derivatives, which are prevalent in the atmosphere and not as relevant in soil. Additionally, PAH products commonly found in the environment can range from as large as five rings to as small as a single ring, requiring a broadly inclusive methodology to comprehensively evaluate mutagenic potential. We developed a combination of supervised and unsupervised machine learning methods to predict environmentally induced PAH mutagenicity with improved performance over currently available tools. K-means clustering with principal component analysis allows us to identify molecular clusters that we hypothesize to have similar mechanisms of action. Recursive feature elimination identifies the most influential descriptors. The cluster-specific regression outperforms available classifiers in predicting direct-acting mutagens resulting from the microbial biodegradation of PAHs and provides direction for future studies evaluating the environmental hazards resulting from PAH biodegradation.
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Affiliation(s)
- Trevor W Sleight
- Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Caitlin N Sexton
- Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Giannis Mpourmpakis
- Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Leanne M Gilbertson
- Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.,Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Carla A Ng
- Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.,Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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47
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Down K, Amour A, Anderson NA, Barton N, Campos S, Cannons EP, Clissold C, Convery MA, Coward JJ, Doyle K, Duempelfeld B, Edwards CD, Goldsmith MD, Krause J, Mallett DN, McGonagle GA, Patel VK, Rowedder J, Rowland P, Sharpe A, Sriskantharajah S, Thomas DA, Thomson DW, Uddin S, Hamblin JN, Hessel EM. Discovery of GSK251: A Highly Potent, Highly Selective, Orally Bioavailable Inhibitor of PI3Kδ with a Novel Binding Mode. J Med Chem 2021; 64:13780-13792. [PMID: 34510892 DOI: 10.1021/acs.jmedchem.1c01102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optimization of a previously reported lead series of PI3Kδ inhibitors with a novel binding mode led to the identification of a clinical candidate compound 31 (GSK251). Removal of an embedded Ames-positive heteroaromatic amine by reversing a sulfonamide followed by locating an interaction with Trp760 led to a highly selective compound 9. Further optimization to avoid glutathione trapping, to enhance potency and selectivity, and to optimize an oral pharmacokinetic profile led to the discovery of compound 31 (GSK215) that had a low predicted daily dose (45 mg, b.i.d) and a rat toxicity profile suitable for further development.
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Affiliation(s)
- Kenneth Down
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Augustin Amour
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Niall A Anderson
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Nick Barton
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Sebastien Campos
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Edward P Cannons
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Cole Clissold
- Charles River Discovery, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Maire A Convery
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - John J Coward
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Kevin Doyle
- Charles River Discovery, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Birgit Duempelfeld
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Christopher D Edwards
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Michael D Goldsmith
- Charles River Discovery, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | - Jana Krause
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - David N Mallett
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Grant A McGonagle
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Vipulkumar K Patel
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - James Rowedder
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Paul Rowland
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Andrew Sharpe
- Charles River Discovery, Chesterford Research Park, Saffron Walden CB10 1XL, U.K
| | | | - Daniel A Thomas
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Douglas W Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Sorif Uddin
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - J Nicole Hamblin
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Edith M Hessel
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K
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48
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Alabi OA, Adeoluwa YM. Mutagenicity and genotoxicity of water boiled in aluminum pots of different duration of use using SOS chromotest and Ames fluctuation test. Toxicol Res (Camb) 2021; 10:771-776. [PMID: 34484668 DOI: 10.1093/toxres/tfab063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 11/14/2022] Open
Abstract
Boiling water before drinking or using it for cooking is a general practice especially in areas where portable water is not readily available. However, boiling water in an aluminum pot could be a route of entry of heavy metals into humans. This study assessed the genotoxic and mutagenic potential of boiled water samples from aluminum pots of different duration of use using the SOS chromotest on Escherichia coli PQ37 and the Ames fluctuation test on Salmonella typhimurium strains TA98 and TA100, respectively. Three aluminum pots from the same manufacturer but of different years of use (6-year-old, 3-year-old, and new aluminum pots) were used for the experiment. Six selected heavy metals (Cadmium, Copper, Arsenic, Nickel, Lead, and Aluminum) were also analyzed in the samples using an Atomic Absorption Spectrophotometer (AAS Buck, Scientific model 210 VGP). Cadmium, Copper, Arsenic, Nickel, Lead, and Aluminum were present in all the test water samples at concentrations that were higher than the maximum limit allowable by standard regulatory organizations. The concentrations of these metals in the samples also increased as the duration of use of the aluminum pots increased. The results further showed that the water boiled in the three aluminum pots is mutagenic and genotoxic in both Ames fluctuation and SOS chromotests. The 6-year-old aluminum pot induced the highest mutagenicity and genotoxicity followed by the 3-year-old aluminum pot. The metals in the tested samples were believed to be responsible for the observed mutagenicity and genotoxicity in the microbial assays. The findings of this study revealed that cooking with Aluminum pots could lead to the leaching of heavy metals into food, and pose mutagenic and genotoxic risks to consumers.
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Affiliation(s)
| | - Yetunde M Adeoluwa
- Department of Biology, Federal University of Technology, Akure, Ondo State, Nigeria
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49
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Assessing the impact of expert knowledge on ICH M7 (Q)SAR predictions. Is expert review still needed? Regul Toxicol Pharmacol 2021; 125:105006. [PMID: 34273441 DOI: 10.1016/j.yrtph.2021.105006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/08/2021] [Accepted: 07/10/2021] [Indexed: 11/21/2022]
Abstract
The ICH M7 (R1) guideline recommends the use of complementary (Q)SAR models to assess the mutagenic potential of drug impurities as a state-of-the-art, high-throughput alternative to empirical testing. Additionally, it includes a provision for the application of expert knowledge to increase prediction confidence and resolve conflicting calls. Expert knowledge, which considers structural analogs and mechanisms of activity, has been valuable when models return an indeterminate (equivocal) result or no prediction (out-of-domain). A retrospective analysis of 1002 impurities evaluated in drug regulatory applications between April 2017 and March 2019 assessed the impact of expert review on (Q)SAR predictions. Expert knowledge overturned the default predictions for 26% of the impurities and resolved 91% of equivocal predictions and 75% of out-of-domain calls. Of the 261 overturned default predictions, 15% were upgraded to equivocal or positive and 79% were downgraded to equivocal or negative. Chemical classes with the most overturns were primary aromatic amines (46%), aldehydes (45%), Michael-reactive acceptors (37%), and non-primary alkyl halides (33%). Additionally, low confidence predictions were the most often overturned. Collectively, the results suggest that expert knowledge continues to play an important role in an ICH M7 (Q)SAR prediction workflow and triaging predictions based on chemical class and probability can improve (Q)SAR review efficiency.
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50
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Categorizing the characteristics of human carcinogens: a need for specificity. Arch Toxicol 2021; 95:2883-2889. [PMID: 34148101 DOI: 10.1007/s00204-021-03109-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023]
Abstract
The International Agency for Research on Cancer (IARC) has recently proposed employing "ten key characteristics of human carcinogens" (TKCs) to determine the potential of agents for harmful effects. The TKCs seem likely to confuse the unsatisfactory correlation from testing regimes that have ignored the differences evident when cellular changes are compared in short and long-lived species, with their very different stem cell and somatic cell phylogenies. The proposed characteristics are so broad that their use will lead to an increase in the current unacceptably high rate of false positives. It could be an informative experiment to take well-established approved therapeutics with well-known human safety profiles and test them against this new TKC paradigm. Cancers are initiated and driven by heritable and transient changes in gene expression, expand clonally, and progress via additional associated acquired mutations and epigenetic alterations that provide cells with an evolutionary advantage. The genotoxicity testing protocols currently employed and required by regulation, emphasize testing for the mutational potential of the test agent. Two-year, chronic rodent cancer bioassays are intended to test for the entire spectrum of carcinogenic transformation. The use of cytotoxic doses causing increased, sustained cell proliferation that facilitates accumulated genetic damage leads to a high false-positive rate of tumor induction. Current cancer hazard assessment protocols and weight-of-the-evidence analysis of agent-specific cancer risk align poorly with the pathogenesis of human carcinoma and so need modernization and improvement in ways suggested here.
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