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Molecular docking and molecular dynamics simulation studies of inhibitor candidates against Anopheles gambiae 3-hydroxykynurenine transaminase and implications on vector control

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Heliyon 2025年第1期11卷 e41633页

作者： Adedeji, Eunice O. Ogunlana, Olubanke O. Oduselu, Gbolahan O. Koenig, Rainer Adebiyi, Ezekiel Soremekun, Opeyemi S. Fatumo, Segun Covenant University Bioinformatics Research (CUBRe) Covenant University Ogun State Ota Nigeria Department of Biochemistry Covenant University Ogun State Ota Nigeria Department of Biology University of York York United Kingdom Covenant Applied Informatics and Communication Africa Centre of Excellence Covenant University Ota Nigeria Institute for Infectious Diseases and Infection Control (IIMK RG Systems Biology) Jena University Hospital Am Klinikum 1 Jena 07747 Germany African Center of Excellence in Bioinformatics & Data Intensive Science Makerere University Kampala 10218 Uganda Division of Applied Bioinformatics German Cancer Research Center (DKFZ) G200 Im Neuenheimer Feld 280 Heidelberg 69120 Germany The African Computational Genomics (TACG) Research Group MRC/UVRI and LSHTM Entebbe Uganda Precision Healthcare University Research Institute Queen Mary University of London United Kingdom Department of Non-Communicable Disease Epidemiology London School of Hygiene & Tropical Medicine United Kingdom

Isoxazole and oxadiazole derivatives inhibiting 3-hydroxykynurenine transaminase (3HKT) are potential larvicidal candidates. This study aims to identify more suited potential inhibitors of Anopheles gambiae 3HKT (Ag3HKT) through molecular docking and molecular dynamics simulation. A total of 958 compounds were docked against Anopheles gambiae 3HKT (PDB ID: 2CH2) using Autodock vina and Autodock4. The top three identified hits were subjected to 300 ns molecular dynamics simulation using AMBER 18 and ADMET analysis using SWISSADME predictor and ADMETSAR. Replacement of alkyl attachment on C5 of isoxazole or oxadiazole derivative with a cycloalkyl group yielded compounds with lower binding energy than their straight chain counterparts. The top three compounds were brominated compounds, 2‐[3‐(4‐bromophenyl)‐1,2‐oxazol‐5‐yl]cyclopentane‐1‐carboxylic acid, 2-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]cyclopentane-1-carboxylic acid, 3-[3-(4-bromo-2-methylphenyl)-1,2,4-oxadiazol-5-yl]cyclopentane-1-carboxylic acid, and they had binding energies of −8.58, −8.25, and −8.18 kcal/mol in virtual screening against 2CH2 protein target, respectively. These compounds were predicted to be less toxic than temephos, a standard larvicide and more biodegradable than previously reported inhibitors. The three compounds exhibited a greater stabilizing effect on 2CH2 protein target than 4-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid, a previously reported inhibitor candidate with good larvicidal activity on Aedes aegypti. Further thermodynamic calculations revealed that the top three compounds possessed total binding energies (ΔG_bind) of −26.64 kcal/mol, −24.26 kcal/mol and −14.11 kcal/mol, respectively, as compared to −12.02 kcal/mol for 4-[3-(4-bromophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid. These compounds could be better larvicides than previously reported isoxazole or oxadiazole derivatives and safer than temephos. © 2025 The Authors

关键词： 1,2,4-Oxadiazole 3HKT Isoxazoles Larvicide Mosquito Vector control

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Arabidopsis EED1 encoding a plant-specific nuclear protein is essential for early embryogenesis

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Journal of Genetics and Genomics 2020年第1期47卷 61-64页

作者： Mai Yang Chun Yan Megan Griffith Jinping Zhao Yongbiao Zhang Daoxin Xie Jianbin Yan MOE Key Laboratory of Bioinformatics Tsinghua-Peking Joint Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine Beihang UniversityBeijing100191China Institute of Molecular and Cell Biology Singapore117609Singapore

Embryogenesis is central to the life cycle of higher plants,which starts from division of the single-cell zygote and culminates in formation of the mature embryo with major cell *** a process generally involves tightl... 详细信息

关键词： formation. Arabidopsis pattern

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FedMonitor: An Implementation Architecture for Monitoring of Resources and Events'Notifications on Federated Cloud Computing Infrastructures 4

FedMonitor: An Implementation Architecture for Monitoring of...

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4th International Conference on Emerging Trends in Networks and Computer Communications, ETNCC 2024

作者： Adetiba, Emmanuel Nnaji, Uche Wejin, John S. Ojesanmi, Festus Akanle, Matthew B. Ajayi, Priscilla O. Sweetwiliams, Faith O. Thakur, Surendra C. Adebiyi, Ezekiel F. Department of Electrical and Information Engineering and Covenant Applied Ota Nigeria HRA Institute for Systems Science Durban University of Technology Durban South Africa Covenant University Department of Computer and Information Science & CApIC-ACE Ota Nigeria Covenant University Department of Electrical and Information Engineering & CApIC-ACE Jalingo Nigeria Tareba State University Department of Computer Science Jalingo Nigeria Ota Nigeria Covenant University & CApIC-ACE Covenant University Department of Electrical and Information Engineering Ota Nigeria Covenant University Center for Systems and Information Services & CApIC-ACE Ota Nigeria Durban University of Technology e-Skills Co-Laboratory Department of Information Technology and KZN Durban4001 South Africa Covenant University Ogun State Ota Nigeria Makerere University African Center of Excellence in Bioinformatics & Data Intensive Science Kampala10218 Uganda

ISBN: (纸本)9798350353266

In the evolving landscape of cloud computing, federated cloud infrastructures present unique challenges and opportunities for resource and application monitoring. Monitoring the diverse array of cloud resources and applications within a federated cloud environment is crucial for delivering consistent Quality of Service (QoS) and continuous oversight across various cloud applications and infrastructure. Despite the various successes documented in the literature on multi-cloud monitoring, existing frameworks have not fully explored or provided enough insights into centralized monitoring of resources, applications, and network devices in a federated cloud environment. This paper introduces FedMonitor, an implementation architecture designed to enhance the monitoring and notification capabilities in federated cloud environments by building on the theoretical ideals in our earlier work (i.e. FEDARGOS-V1). FedMonitor leverages Prometheus and Grafana to crawl, manage and visualize metrics from diverse software services, hardware resources, and network devices within a federated cloud environment. The results demonstrate hat FedMonitor improves the effectiveness of resource and application monitoring in federated cloud environments. © 2024 IEEE.

关键词： Cloud platforms

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Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development

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Scientific Reports 2025年第1期15卷 1-18页

作者： Okafor, Adaobi Adam, Yagoub Brors, Benedikt Adebiyi, Ezekiel Applied Bioinformatics German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 Heidelberg 69120 Germany Faculty of Biosciences Heidelberg University Im Neuenheimer Feld 234 Heidelberg 69120 Germany Covenant University Bioinformatics Research (CUBRe) Covenant University Ogun State Ota 112233 Nigeria African Center of Excellence in Bioinformatics & Data Intensive Science Makerere University Kampala 10218 Uganda Institute of Infectious Diseases (IDI) Makerere University Kampala 10218 Uganda

The life cycle of Plasmodium parasites involves intricate, multistage processes that are tightly regulated by stage-specific transcription factors. These factors bind to regulatory regions within gene promoters, enabling the precise expression of genes required for each developmental stage. Despite the importance of these transcriptional mechanisms, our understanding remains limited, particularly in the rodent model organism P. berghei. To address this, we conducted a genome-wide analysis of RNA-Seq data from different developmental stages of P. berghei by initially integrating data from human malaria parasites P. falciparum and P. vivax. We identified unique transcriptional signatures across Plasmodium species. Our analysis of P. berghei revealed stage-specific gene sets clustered by expression profiles and predicted regulatory motifs involved in their control. We interpreted these motifs using known binding sites for eukaryotic transcription factors including ApiAP2 proteins. Additionally, we expanded the annotation of the AGGTAA motif which resembles a de novo motif linked to erythrocytic development in P. falciparum, and identified its potential interacting proteins including members of the PfMORC and GCN5 complexes. This study enhances our understanding of gene regulation in P. berghei and provides new insights into the transcriptional dynamics underlying Plasmodium development. © The Author(s) 2025.

关键词： ApiAP2 proteins Plasmodium berghei Plasmodium falciparum Plasmodium vivax Regulatory motifs RNA-Seq

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MassSpecGym: a benchmark for the discovery and identification of molecules 24

MassSpecGym: a benchmark for the discovery and identificatio...

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Proceedings of the 38th International Conference on Neural Information Processing Systems

作者： Roman Bushuiev Anton Bushuiev Niek F. de Jonge Adamo Young Fleming Kretschmer Raman Samusevich Janne Heirman Fei Wang Luke Zhang Kai Dührkop Marcus Ludwig Nils A. Haupt Apurva Kalia Corinna Brungs Robin Schmid Russell Greiner Bo Wang David S. Wishart Li-Ping Liu Juho Rousu Wout Bittremieux Hannes Rost Tytus D. Mak Soha Hassoun Florian Huber Justin J.J. van der Hooft Michael A. Stravs Sebastian Böcker Josef Sivic Tomáš Pluskal Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Czech Institute of Informatics Robotics and Cybernetics Czech Technical University Czech Institute of Informatics Robotics and Cybernetics Czech Technical University Bioinformatics Group Wageningen University & Research Department of Computer Science University of Toronto Chair for Bioinformatics Institute for Computer Science Friedrich Schiller University Jena Department of Computer Science University of Antwerp Department of computing science University of Alberta and Alberta Machine Intelligence Institute Department of Molecular Genetics University of Toronto Bright Giant GmbH Department of Computer Science Tufts University Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Department of computing science and Department of Biological Sciences University of Alberta Department of Computer Science Aalto University Mass Spectrometry Data Center National Institute of Standards and Technology Department of Computer Science and Department of Chemical and Biological Engineering Tufts University Centre for Digitalisation and Digitality University of Applied Sciences Düsseldorf Bioinformatics Group Wageningen University & Research and Department of Biochemistry University of Johannesburg Eawag: Swiss Federal Institute of Aquatic Science and Technology

ISBN: (纸本)9798331314385

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym - the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://***/pluskal-lab/MassSpecGym.

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Prenatal exposure to parabens in relation to childhood obesity and the gut microbiome

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Taiwan Journal of Public Health 2023年第1期42卷 62-74页

作者： Chen, Ying Kuo, Chin-Chi Chen, Ting-Wen Wang, Shu-Li Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Big Data Center China Medical University Hospital Taichung Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu Taiwan National Institute of Environmental Health Sciences National Health Research Institutes No. 35 Keyan Rd Zhunan Town Miaoli Taiwan Department of Public Health National Defence Medical Centre Taipei Taiwan

Objectives: Parabens, which are common antimicrobial preservatives, are considered to be endocrine-disrupting chemicals. Previous studies regarding maternal exposure to paraben have shown that disturbances in physiological endocrine and metabolic signals during early childhood may lead to the long-term adverse health effects in children. We investigated the effects of maternal exposure to paraben on childhood obesity and gut microbiome diversity. Methods: We collected the data on 284 maternalinfant pairs from the central region of Taiwan Maternal- Infant Cohort Study. Liquid chromatography-tandem mass spectrometry was used to detect 4 common parabens, including methyl-paraben, ethyl-paraben, propyl-paraben, and butyl-paraben in maternal urinary samples. In addition, shotgun metagenomics sequencing was used to analyze 98 children’s fecal samples. Results: Greater maternal exposure to paraben was observed in boys who were significantly shorter and with wider chest circumferences and in girls with higher body mass index. Increased maternal exposure to paraben significantly reduced the abundance of several species, such as Barnesiella, Bacteroides uniformis, and Eubacterium rectale, but increased the abundance of several opportunistic pathogens, which interfered with the regulation of energy consumption. Conclusions: Maternal exposure to paraben promoted the development of obesity in girls and disrupted the diversity of gut microbial community. Maternal exposure to paraben may promote obesity in children at preschooler age. In addition, additional studies on the effects of the composition of the gut microbiome after puberty are required. © 2023, Taiwan Public Health Association. All rights reserved.

关键词： childhood obesity gut microbiome parabens prenatal exposure

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database management system design for automatic weather information with twitter data collection 6

Database management system design for automatic weather info...

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6th International Conference on Information Management and Technology, ICIMTech 2021

作者： Purwandari, Kartika Perbangsa, Anzaludin Samsinga Sigalingging, Join W. C. Krisna, Adhi Asta Anggrayani, Suci Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University School of Information Systems Information Systems Department Jakarta11480 Indonesia Meteorological Climatological and Geophysical Agency Database Center Division of Bmkg Jakarta10720 Indonesia Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665449373

Improvement of data management about weather in Indonesia is very supportive of the need for weather information. Currently, the weather information that is disseminated to the public is only based on sensor location points that are spread across Indonesia. However, supporting data generated from these sensors is only limited to certain areas. We hence develop a database system that can help collect weather information automatically via Twitter. This facilitates the Indonesian people in knowing weather information based on the completeness of data from sensor data and Twitter. The steps from the database that are built will be very helpful in collecting data about the weather throughout Indonesia. The basic step that we use in our database are conceptual, logical and physical design. The information obtained in this study is very important for efficient and effective data collection to achieve real-time automation of weather information. © 2021 IEEE.

关键词： database systems

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Comparative study between molecular and genetic evolutionary analysis tools using African SARS-CoV-2 variants

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Informatics in Medicine Unlocked 2023年 36卷

作者： Awe, Olaitan I. En najih, Nouhaila Nyamari, Marion N. Mukanga, Latifah B. Department of Computer Science University of Ibadan Oyo State Ibadan Nigeria African Society for Bioinformatics and Computational Biology South Africa Systems and Data Engineering Team National School of Applied Sciences Abdelmalek Essaadi University Tangier Morocco School of Pure and Applied Sciences Pwani University Kenya Department of Life Sciences South Eastern Kenya University Kitui Kenya

Phylogenetic analysis is one of the most reliable and important analyses in bioinformatics. Currently, many phylogenetic analysis tools can be used for the visualization and interpretation of biological data. However, a lot of technical expertise is required in order to use these tools. It is challenging for biologists to have to deal with this issue. This study therefore compared three multipurpose phylogenetic analysis tools and informed on their features so as to help the user choose the appropriate tool for their research and resources, especially those who want to do research in bioinformatics in Africa. Phylogenetic analysis was done on whole genome sequences obtained from NCBI repositories using MEGA, SeaView and Geneious separately. Subsequently, a detailed comparison table based on features for each tool was generated. What makes our study unique is that we used the African SARS-CoV-2 genomes which have rarely been used for studies describing the evolution of coronaviruses. After the benchmarking, we recommend tools based on the user's resources and objectives. MEGA and SeaView would be the best option for a researcher with no technical bioinformatics knowledge and looking for a free tool. Geneious is as easy to use as MEGA and SeaView, and it additionally gives more options and information. On the other hand, it requires a lot of time and it is not free to use. We have highlighted the relevant molecular and genetic evolutionary analysis tool based on the user's resources. © 2022 The Authors

关键词： Geneious MEGA Phylogenetic analysis SARS-CoV-2 SeaView

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787 IL-33 signals through a novel ST2-independent pathway to modulate barrier function in human skin

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Journal of Investigative Dermatology 2023年第5期143卷 S135-S135页

作者： N. Hawkshaw S. Sagawe S. Monkley C. Morton I. Dillmann J. Lindgren V. Augusti Negri R. Chen X. Romero Ros S. Cohen Bioscience Asthma & Skin Immunity Data Science & Bioinformatics Translational Genomics Precision Medicine Discovery BioPharmaceuticals R&D AstraZeneca Cambridge United Kingdom

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Fine-scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing

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植物分类学报 2021年第1期59卷 1-20页

作者： Guang-Lin He Ying-Xiang Li Meng-Ge Wang Xing Zou Hui-Yuan Yeh Xiao-Min Yang Zheng Wang Ren-Kuan Tang Su-Min Zhu Jian-Xin Guo Ting Luo Jing Zhao Jin Sun Zi-Yang Xia Hao-Liang Fan Rong Hu Lan-Hai Wei Gang Chen Yi-Ping Hou Chuan-Chao Wang Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China School of Humanities Nanyang Technological UniversityNanyang 639798Singapore Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China Department of Forensic Medicine College of Basic Medicine Chongqing Medical UniversityChongqing 400000China Department of Forensic Medicine College of Basic Medicine Chongqing Medical UniversityChongqing 400000China Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Department of Anthropology and Ethnology In

Archaeological,genetic,and linguistic evidence has supported the idea that northern China is the original center of modern Sino-Tibetan-speaking ***,the demographic history of subsequent southward migration and genetic admixture of Han Chinese with surrounding indigenous populations remain uncharacterized,and the language shifts and assimilations accompanied by movement of people,or just an adaptation of cultural ideas among populations in central China is still unclear,especially for Tibeto-Burman-speaking Tujia and central Han Chinese *** resolve this,we genotyped over 60K genome-wide markers in 505 unrelated individuals from 63 indigenous *** results showed both studied Han and Tujia were at the intermediate position in the modern East Asian North-South genetic cline and there was a correlation between the genetic composition and the *** observed the strong genetic assimilation between Tujia people and central Han Chinese,which suggested massive population movements and genetic admixture under language *** and central Han Chinese could be modeled as a two-way admixture deriving primary ancestry from a northern ancestral population closely related to the ancient DevilsCave and present-day Tibetans and a southern ancestral population closely related to the present-day Tai-Kadai and Austronesian-speaking *** ancestral northern population we suspect to be related to the Neolithic millet farming groups in the Yellow River Basin or central *** showed that the newly genotyped populations in Hubei Province had a higher proportion of DevilsCave or modern Tungusic/Mongolic-related northern ancestries,while the Hunan populations harbored a higher proportion of Austronesian/Tai-Kadai-related southern ancestries.

关键词： demographic history gene flow genetic admixture language borrowing Tibeto-Burman Tujia

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