1
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Ballweg T, Liu M, Mama A, Wenzel W, Franzreb M. Molecular insights into chromatography: Automated workflows for the virtual design of methacrylate-based chromatography resins. J Chromatogr A 2025; 1754:466027. [PMID: 40367847 DOI: 10.1016/j.chroma.2025.466027] [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: 02/08/2025] [Revised: 04/14/2025] [Accepted: 05/06/2025] [Indexed: 05/16/2025]
Abstract
Computational chemistry provides invaluable insights into the behaviors and properties of various materials at the molecular level. This capability is of particular interest in chromatography where adsorbents engage with target molecules through intricate interactions. However, the broad integration of molecular simulations into the field of chromatography has been notably limited, despite significant achievements in previous studies. One potential reason is the requirement for considerable expertise to effectively configure these simulations, presenting a significant barrier to entry. In this context, workflow management systems (WMSs) provide a viable solution by allowing experts to automate complex simulation tasks, making them accessible to the wider research community without necessitating in-depth knowledge of the simulation process. This manuscript outlines the creation and application of two automated workflows designed to generate comprehensive all-atom models of methacrylate-based chromatography resin surfaces and to rapidly calculate binding free energies with peptides as target molecules. These innovations represent a significant advancement in the field by streamlining the simulation process, enhancing predictive accuracy, and making complex molecular modeling more accessible to researchers across disciplines. By publishing these workflows, we aim to catalyze molecular modeling in the field of chromatography by encouraging scientists to utilize and build upon our work.
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Affiliation(s)
- Tim Ballweg
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Modan Liu
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ahmed Mama
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Matthias Franzreb
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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2
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Kurz NS, Kornrumpf K, Tucholski T, Drofenik K, König A, Beißbarth T, Dönitz J. Onkopus: precise interpretation and prioritization of sequence variants for biomedical research and precision medicine. Nucleic Acids Res 2025:gkaf376. [PMID: 40377094 DOI: 10.1093/nar/gkaf376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Revised: 04/14/2025] [Accepted: 04/25/2025] [Indexed: 05/18/2025] Open
Abstract
One of the major challenges in precision oncology is the identification of pathogenic, actionable variants and the selection of personalized treatments. We present Onkopus, a variant interpretation framework based on a modular architecture, for interpreting and prioritizing genetic alterations in cancer patients. A multitude of tools and databases are integrated into Onkopus to provide a comprehensive overview about the consequences of a variant, each with its own semantic, including pathogenicity predictions, allele frequency, biochemical and protein features, and therapeutic options. We present the characteristics of variants and personalized therapies in a clear and concise form, supported by interactive plots. To support the interpretation of variants of unknown significance (VUS), we present a protein analysis based on protein structures, which allows variants to be analyzed within the context of the entire protein, thereby serving as a starting point for understanding the underlying causes of variant pathogenicity. Onkopus has the potential to significantly enhance variant interpretation and the selection of actionable variants for identifying new targets, drug screens, drug testing using organoids, or personalized treatments in molecular tumor boards. We provide a free public instance of Onkopus at https://mtb.bioinf.med.uni-goettingen.de/onkopus.
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Affiliation(s)
- Nadine S Kurz
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany
- Göttingen Comprehensive Cancer Center (G-CCC), 37075 Göttingen, Germany
| | - Kevin Kornrumpf
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Tim Tucholski
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany
- Institute of Pathology, University Medical Center Göttingen , 37075 Göttingen, Germany
| | - Klara Drofenik
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany
- Göttingen Comprehensive Cancer Center (G-CCC), 37075 Göttingen, Germany
| | - Alexander König
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Tim Beißbarth
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany
- Göttingen Comprehensive Cancer Center (G-CCC), 37075 Göttingen, Germany
- Campus Institute Data Science (CIDAS), Section Medical Data Science (MeDaS), 37077 Göttingen, Germany
| | - Jürgen Dönitz
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany
- Göttingen Comprehensive Cancer Center (G-CCC), 37075 Göttingen, Germany
- Campus Institute Data Science (CIDAS), Section Medical Data Science (MeDaS), 37077 Göttingen, Germany
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3
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Schimunek J, Luukkonen S, Klambauer G. MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery. J Chem Inf Model 2025; 65:4243-4250. [PMID: 40302701 PMCID: PMC12076497 DOI: 10.1021/acs.jcim.4c02373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 04/09/2025] [Accepted: 04/10/2025] [Indexed: 05/02/2025]
Abstract
Today's drug discovery increasingly relies on computational and machine learning approaches to identify novel candidates, yet data scarcity remains a significant challenge. To address this limitation, we present MHNfs, an application specifically designed to predict molecular activity in low-data scenarios. At its core, MHNfs leverages a state-of-the-art few-shot activity prediction model, named MHNfs, which has demonstrated strong performance across a large set of prediction tasks in the benchmark data set FS-Mol. The application features an intuitive interface that enables users to prompt the model for precise activity predictions based on a small number of known active and inactive molecules, akin to interactive interfaces for large language models. To evaluate its efficacy, we simulate real-world scenarios by recasting PubChem bioassays as few-shot prediction tasks. MHNfs offers a streamlined and accessible solution for deploying advanced few-shot learning models, providing a valuable tool for accelerating drug discovery.
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Affiliation(s)
- Johannes Schimunek
- ELLIS Unit Linz and LIT AI Lab, Institute
for Machine Learning, Johannes Kepler University
Linz, A-4040 Linz, Austria
| | - Sohvi Luukkonen
- ELLIS Unit Linz and LIT AI Lab, Institute
for Machine Learning, Johannes Kepler University
Linz, A-4040 Linz, Austria
| | - Günter Klambauer
- ELLIS Unit Linz and LIT AI Lab, Institute
for Machine Learning, Johannes Kepler University
Linz, A-4040 Linz, Austria
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4
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Astolfi A, Cernicchi G, Primavera E, Rocchi M, Manfroni G, Sabatini S, Letizia Barreca M. Addressing Data Point Homogeneity and Annotation Challenges to Enhance Data-Driven Approaches: The S. aureus NorA Efflux Pump Case Study. ChemMedChem 2025; 20:e202400927. [PMID: 39843395 DOI: 10.1002/cmdc.202400927] [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: 11/16/2024] [Revised: 01/15/2025] [Accepted: 01/20/2025] [Indexed: 01/24/2025]
Abstract
In this study, we analyzed publicly accessible data related to the Staphylococcus aureus NorA protein, a well-known efflux pump involved in antimicrobial resistance. Our analysis revealed several inconsistencies in data annotation, and significant issues concerning the homogeneity across datasets, which compromise the reliability of data-driven approaches aimed at identifying novel Staphylococcus aureus NorA efflux pump inhibitors (EPIs). To address these challenges, we propose a standardized pipeline for experimental procedures and data annotation, designed to enhance the consistency and quality of EPI datasets submitted to repositories, thereby increasing the utility of publicly available datasets for the discovery of potential EPIs. By implementing this framework, the findings reported herein aim to foster more reliable and reproducible research outcomes in drug discovery projects targeting NorA or other efflux pumps.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Giada Cernicchi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Erika Primavera
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
- Sibylla Biotech S.p.A., Via Lillo del Duca 10, 20091, Bresso, Italy
| | - Marco Rocchi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
- Innovatune S.r.l., Via Giulio Zanon 130/D, 35129, Padova, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
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5
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Zhao Y, Cao LY, Zhao YX, Zhao D, Huang YF, Wang F, Wang Q. Harnessing Risk Assessment for Thrombosis and Bleeding to Optimize Anticoagulation Strategy in Nonvalvular Atrial Fibrillation. Thromb Haemost 2025; 125:492-504. [PMID: 39137902 PMCID: PMC12040435 DOI: 10.1055/a-2385-1452] [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: 08/04/2024] [Indexed: 08/15/2024]
Abstract
Oral anticoagulation (OAC) following catheter ablation (CA) of nonvalvular atrial fibrillation (NVAF) is essential for the prevention of thrombosis events. Inappropriate application of OACs does not benefit stroke prevention but may be associated with a higher risk of bleeding. Therefore, this study aims to develop clinical data-driven machine learning (ML) methods to predict the risk of thrombosis and bleeding to establish more precise anticoagulation strategies for patients with NVAF.Patients with NVAF who underwent CA therapy were enrolled from Southwest Hospital from 2015 to 2023. This study compared eight ML algorithms to evaluate the predictive power for both thrombosis and bleeding. Model interpretations were recognized by feature importance and SHapley Additive exPlanations methods. With potential essential risk factors, simplified ML models were proposed to improve the feasibility of the tool.A total of 1,055 participants were recruited, including 105 patients with thrombosis and 252 patients with bleeding. The models based on XGBoost achieved the best performance with accuracies of 0.740 and 0.781 for thrombosis and bleeding, respectively. Age, BNP, and the duration of heparin are closely related to the high risk of thrombosis, whereas the anticoagulation strategy, BNP, and lipids play a crucial role in the occurrence of bleeding. The optimized models enrolling crucial risk factors, RF-T for thrombosis and Xw-B for bleeding, achieved the best recalls of 0.774 and 0.780, respectively.The optimized models will have a great application potential in predicting thrombosis and bleeding among patients with NVAF and will form the basis for future score scales.
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Affiliation(s)
- Yue Zhao
- Department of Pharmacy, The First Affiliated Hospital of Army Medical University (Third Military Medical University), Chongqing, P. R. China
| | - Li-Ya Cao
- Department of Pharmacy, The First Affiliated Hospital of Army Medical University (Third Military Medical University), Chongqing, P. R. China
| | - Ying-Xin Zhao
- Department of Pharmacy, Army Medical Center, Army Medical University (Third Military Medical University), Chongqing, P. R. China
| | - Di Zhao
- Department of Pharmacy, The First Affiliated Hospital of Army Medical University (Third Military Medical University), Chongqing, P. R. China
| | - Yi-Fan Huang
- Medical Big Data and Artificial Intelligence Center, The First Affiliated Hospital of Army Medical University (Third Military Medical University), Chongqing, PR China
| | - Fei Wang
- Medical Big Data and Artificial Intelligence Center, The First Affiliated Hospital of Army Medical University (Third Military Medical University), Chongqing, PR China
| | - Qian Wang
- Department of Pharmacy, The First Affiliated Hospital of Army Medical University (Third Military Medical University), Chongqing, P. R. China
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6
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Steinbeck C. The evolution of open science in cheminformatics: a journey from closed systems to collaborative innovation. J Cheminform 2025; 17:44. [PMID: 40181430 PMCID: PMC11969984 DOI: 10.1186/s13321-025-00990-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Accepted: 03/19/2025] [Indexed: 04/05/2025] Open
Abstract
Cheminformatics has significantly transformed over the past four decades, evolving from a field dominated by proprietary systems to one increasingly embracing open science principles. In its early years, cheminformatics was characterised by commercial software and restricted data access, limiting collaboration and reproducibility. The advent of open-source software in the late 1990s and early 2000s, including tools such as the Chemistry Development Kit (CDK) and RDKit, played a crucial role in democratising computational chemistry. Open data initiatives, such as PubChem and NMRShiftDB, further enhanced accessibility by providing freely available chemical information, fostering transparency and interoperability and introducing key standards, such as the International Chemical Identifier (InChI), revolutionised data integration and retrieval across diverse platforms. Community-driven efforts, including the Blue Obelisk movement and Open Notebook Science, have promoted open methodologies and collaborative research. More recently, national data infrastructure projects like NFDI4Chem have aimed to standardise research data management in cheminformatics, ensuring the long-term sustainability of open science practices. The increasing adoption of the FAIR (Findable, Accessible, Interoperable, Reusable) principles has further reinforced data sharing and reuse in computational chemistry. Challenges remain, particularly in overcoming resistance to data sharing and ensuring sustainable funding for open projects. However, the trajectory of cheminformatics demonstrates that embracing openness enhances scientific integrity and accelerates discovery and innovation.
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Affiliation(s)
- Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Jena, Germany.
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7
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Ge W, De Silva R, Fan Y, Sisson SA, Stenzel MH. Machine Learning in Polymer Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2025; 37:e2413695. [PMID: 39924835 PMCID: PMC11923530 DOI: 10.1002/adma.202413695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 12/21/2024] [Indexed: 02/11/2025]
Abstract
Machine learning is increasingly being applied in polymer chemistry to link chemical structures to macroscopic properties of polymers and to identify chemical patterns in the polymer structures that help improve specific properties. To facilitate this, a chemical dataset needs to be translated into machine readable descriptors. However, limited and inadequately curated datasets, broad molecular weight distributions, and irregular polymer configurations pose significant challenges. Most off the shelf mathematical models often need refinement for specific applications. Addressing these challenges demand a close collaboration between chemists and mathematicians as chemists must formulate research questions in mathematical terms while mathematicians are required to refine models for specific applications. This review unites both disciplines to address dataset curation hurdles and highlight advances in polymer synthesis and modeling that enhance data availability. It then surveys ML approaches used to predict solid-state properties, solution behavior, composite performance, and emerging applications such as drug delivery and the polymer-biology interface. A perspective of the field is concluded and the importance of FAIR (findability, accessibility, interoperability, and reusability) data and the integration of polymer theory and data are discussed, and the thoughts on the machine-human interface are shared.
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Affiliation(s)
- Wei Ge
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
- School of Mathematics and Statistics and UNSW Data Science Hub, University of New South Wales, Sydney, 2052, Australia
| | - Ramindu De Silva
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
- School of Mathematics and Statistics and UNSW Data Science Hub, University of New South Wales, Sydney, 2052, Australia
- Data61, CSIRO, Sydney, NSW, 2015, Australia
| | - Yanan Fan
- School of Mathematics and Statistics and UNSW Data Science Hub, University of New South Wales, Sydney, 2052, Australia
- Data61, CSIRO, Sydney, NSW, 2015, Australia
| | - Scott A Sisson
- School of Mathematics and Statistics and UNSW Data Science Hub, University of New South Wales, Sydney, 2052, Australia
| | - Martina H Stenzel
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
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8
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Malashin I, Tynchenko V, Gantimurov A, Nelyub V, Borodulin A. Support Vector Machines in Polymer Science: A Review. Polymers (Basel) 2025; 17:491. [PMID: 40006153 PMCID: PMC11859395 DOI: 10.3390/polym17040491] [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: 01/06/2025] [Revised: 02/06/2025] [Accepted: 02/11/2025] [Indexed: 02/27/2025] Open
Abstract
Polymer science, a discipline focusing on the synthesis, characterization, and application of macromolecules, has increasingly benefited from the adoption of machine learning (ML) techniques. Among these, Support Vector Machines (SVMs) stand out for their ability to handle nonlinear relationships and high-dimensional datasets, which are common in polymer research. This review explores the diverse applications of SVM in polymer science. Key examples include the prediction of mechanical and thermal properties, optimization of polymerization processes, and modeling of degradation mechanisms. The advantages of SVM are contrasted with its challenges, including computational cost, data dependency, and the need for hyperparameter tuning. Future opportunities, such as the development of polymer-specific kernels and integration with real-time manufacturing systems, are also discussed.
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Affiliation(s)
- Ivan Malashin
- Artificial Intelligence Technology Scientific and Education Center, Bauman Moscow State Technical University, 105005 Moscow, Russia
| | - Vadim Tynchenko
- Artificial Intelligence Technology Scientific and Education Center, Bauman Moscow State Technical University, 105005 Moscow, Russia
| | - Andrei Gantimurov
- Artificial Intelligence Technology Scientific and Education Center, Bauman Moscow State Technical University, 105005 Moscow, Russia
| | - Vladimir Nelyub
- Artificial Intelligence Technology Scientific and Education Center, Bauman Moscow State Technical University, 105005 Moscow, Russia
- Scientific Department, Far Eastern Federal University, 690922 Vladivostok, Russia
| | - Aleksei Borodulin
- Artificial Intelligence Technology Scientific and Education Center, Bauman Moscow State Technical University, 105005 Moscow, Russia
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9
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Zhang D, Deacon BN, Li W, Lian G, Chen T. A computational workflow for end-to-end simulation of percutaneous absorption. Int J Pharm 2025; 670:125084. [PMID: 39681219 DOI: 10.1016/j.ijpharm.2024.125084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 11/29/2024] [Accepted: 12/11/2024] [Indexed: 12/18/2024]
Abstract
PURPOSE Presented is the development of a workflow for end-to-end (e2e) in silico modelling of percutaneous absorption under a range of test conditions, integrating multiple calculation and analysis steps for in-silico simulation of dermal absorption. The aim is to achieve a digital twin that can be used by non-modelling experts to simulate transdermal permeation. METHODS A KNIME-based toolbox is used to create the workflow for the E2E in-silico model. The workflow first combines physicochemical property informatics (ChemAxon), molecular dynamics (MD) modelling, and quantitative structure-property relations (QSPRs) to calculate the diffusion and partition properties of permeants in heterogeneous skin layers and complex formulation vehicles. These are then set as input parameters to physiologically based pharmacokinetics (PBPK) model to simulate percutaneous absorption under complex in vitro testing or in vivo exposure conditions set by the end user. Integrated into the PBPK model is the evaporation of volatile permeants and solvents for in vitro unoccluded conditions. The workflow generates a report of the results and records the tested formulation in a database. RESULTS The workflow has been tested against several sets of published in vitro permeation test (IVPT) results of percutaneous absorption involving different formulation vehicles. The model predictions of formulation and evaporation effects on percutaneous absorption agreed well with experimental data. CONCLUSIONS By automating multiple calculation steps from permeant property, diffusion-partition skin layers and formulation vehicles, to PBPK modelling of dermal absorption, the workflow provides a user-friendly means for non-modelling experts to conduct in-silico simulations of transdermal absorption under various conditions. The workflow is robust to simulate the impact of complex formulation and exposure conditions including evaporation of volatile permeants and solvents on the delivery into the skin.
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Affiliation(s)
- Duo Zhang
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, UK
| | - Benjamin N Deacon
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, UK
| | - Weijun Li
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, UK
| | - Guoping Lian
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, UK; Unilever R&D Colworth, Unilever, Sharnbrook MK44 1LQ, UK.
| | - Tao Chen
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford GU2 7XH, UK
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10
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Camci M, Şenol H, Kose A, Karaman Mayack B, Alayoubi MM, Karali N, Gezginci MH. Bioisosteric replacement of the carboxylic acid group in Hepatitis-C virus NS5B thumb site II inhibitors: phenylalanine derivatives. Eur J Med Chem 2024; 279:116832. [PMID: 39288595 DOI: 10.1016/j.ejmech.2024.116832] [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: 07/11/2023] [Revised: 11/03/2023] [Accepted: 09/01/2024] [Indexed: 09/19/2024]
Abstract
Hepatitis C virus (HCV) is a global health concern and the NS5B RNA-dependent RNA polymerase (RdRp) of HCV is an attractive target for drug discovery due to its role in viral replication. This study focuses on NS5B thumb site II inhibitors, specifically phenylalanine derivatives, and explores bioisosteric replacement and prodrug strategies to overcome limitations associated with carboxylic acid functionality. The synthesized compounds demonstrated antiviral activity, with compound 6d showing the most potent activity with an EC50 value of 3.717 μM. The hydroxamidine derivatives 7a-d showed EC50 values ranging from 3.9 μM to 11.3 μM. However, the acidic heterocyclic derivatives containing the oxadiazolone (8a-d) and oxadiazolethione (9a-d) rings did not exhibit measurable activity. A methylated heterocycle 10b showed a hint of activity at 8.09 μM. The pivaloyloxymethyl derivatives 11a and 11b did not show antiviral activity. Further studies are warranted to fully understand the effects of these modifications and to explore additional strategies for developing novel therapeutic options for HCV.
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Affiliation(s)
- Merve Camci
- Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34116, Istanbul, Turkey; Graduate School of Health Sciences, Istanbul University, 34126, Istanbul, Turkey.
| | - Halil Şenol
- Bezmialem Vakif University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34093, Istanbul, Turkey.
| | - Aytekin Kose
- Aksaray University, Faculty of Science and Letters, Department of Chemistry, 68100, Aksaray, Turkey.
| | - Berin Karaman Mayack
- Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34116, Istanbul, Turkey; Department of Pharmacology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
| | | | - Nilgun Karali
- Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34116, Istanbul, Turkey.
| | - Mikail Hakan Gezginci
- Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34116, Istanbul, Turkey.
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11
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Luo Y, Zhao C, Chen F. Multiomics Research: Principles and Challenges in Integrated Analysis. BIODESIGN RESEARCH 2024; 6:0059. [PMID: 39990095 PMCID: PMC11844812 DOI: 10.34133/bdr.0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 02/25/2025] Open
Abstract
Multiomics research is a transformative approach in the biological sciences that integrates data from genomics, transcriptomics, proteomics, metabolomics, and other omics technologies to provide a comprehensive understanding of biological systems. This review elucidates the fundamental principles of multiomics, emphasizing the necessity of data integration to uncover the complex interactions and regulatory mechanisms underlying various biological processes. We explore the latest advances in computational methodologies, including deep learning, graph neural networks (GNNs), and generative adversarial networks (GANs), which facilitate the effective synthesis and interpretation of multiomics data. Additionally, this review addresses the critical challenges in this field, such as data heterogeneity, scalability, and the need for robust, interpretable models. We highlight the potential of large language models to enhance multiomics analysis through automated feature extraction, natural language generation, and knowledge integration. Despite the important promise of multiomics, the review acknowledges the substantial computational resources required and the complexity of model tuning, underscoring the need for ongoing innovation and collaboration in the field. This comprehensive analysis aims to guide researchers in navigating the principles and challenges of multiomics research to foster advances in integrative biological analysis.
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Affiliation(s)
- Yunqing Luo
- National Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571700, China
| | - Chengjun Zhao
- National Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571700, China
| | - Fei Chen
- National Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China
- College of Tropical Agriculture and Forestry, Hainan University, Danzhou 571700, China
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12
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Pekdas IG, Uflaz E, Tornacı F, Arslan O, Turan O. Developing a machine learning-based evaluation system for the recruitment of maritime professionals. OCEAN ENGINEERING 2024; 313:119406. [DOI: 10.1016/j.oceaneng.2024.119406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
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13
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Henkel M, Fillbrunn A, Marchand V, Raghunathan G, Berthold MR, Motorin Y, Marx A. A DNA Polymerase Variant Senses the Epigenetic Marker 5-Methylcytosine by Increased Misincorporation. Angew Chem Int Ed Engl 2024; 63:e202413304. [PMID: 39449390 DOI: 10.1002/anie.202413304] [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: 07/15/2024] [Indexed: 10/26/2024]
Abstract
Dysregulation of DNA methylation is associated with human disease, particularly cancer, and the assessment of aberrant methylation patterns holds great promise for clinical diagnostics. However, DNA polymerases do not effectively discriminate between processing 5-methylcytosine (5 mC) and unmethylated cytosine, resulting in the silencing of methylation information during amplification or sequencing. As a result, current detection methods require multi-step DNA conversion treatments or careful analysis of sequencing data to decipher individual 5 mC bases. To overcome these challenges, we propose a novel DNA polymerase-mediated 5 mC detection approach. Here, we describe the engineering of a thermostable DNA polymerase variant derived from Thermus aquaticus with altered fidelity towards 5 mC. Using a screening-based evolutionary approach, we have identified a DNA polymerase that exhibits increased misincorporation towards 5 mC during DNA synthesis. This DNA polymerase generates mutation signatures at methylated CpG sites, allowing direct detection of 5 mC by reading an increased error rate after sequencing without prior treatment of the sample DNA.
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Affiliation(s)
- Melanie Henkel
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Alexander Fillbrunn
- Department of Computer Science, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Virginie Marchand
- Epitranscriptomics and Sequencing (EpiRNA-Seq) Core Facility, UAR2008/US40 Ingénierie Biologie Santé en Lorraine (IBSLor), CNRS-UL-INSERM, Université de Lorraine, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandoeuvre-les-Nancy, France
| | - Govindan Raghunathan
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Michael R Berthold
- Department of Computer Science, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
- KNIME AG, Talacker 50, 8001, Zurich, Switzerland
| | - Yuri Motorin
- Epitranscriptomics and Sequencing (EpiRNA-Seq) Core Facility, UAR2008/US40 Ingénierie Biologie Santé en Lorraine (IBSLor), CNRS-UL-INSERM, Université de Lorraine, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandoeuvre-les-Nancy, France
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR7365 CNRS-Université de Lorraine, Université de Lorraine, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandoeuvre-les-Nancy, France
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
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14
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Aksenova A, Johny A, Adams T, Gribbon P, Jacobs M, Hofmann-Apitius M. Current state of data stewardship tools in life science. Front Big Data 2024; 7:1428568. [PMID: 39351001 PMCID: PMC11439729 DOI: 10.3389/fdata.2024.1428568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 08/23/2024] [Indexed: 10/04/2024] Open
Abstract
In today's data-centric landscape, effective data stewardship is critical for facilitating scientific research and innovation. This article provides an overview of essential tools and frameworks for modern data stewardship practices. Over 300 tools were analyzed in this study, assessing their utility, relevance to data stewardship, and applicability within the life sciences domain.
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Affiliation(s)
- Anna Aksenova
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Bonn, Germany
| | - Anoop Johny
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
| | - Tim Adams
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
| | - Phil Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology, Discovery Research Screening Port, Hamburg, Germany
| | - Marc Jacobs
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
| | - Martin Hofmann-Apitius
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Bonn, Germany
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
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15
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Keikhosravi A, Almansour F, Bohrer CH, Fursova NA, Guin K, Sood V, Misteli T, Larson DR, Pegoraro G. High-throughput image processing software for the study of nuclear architecture and gene expression. Sci Rep 2024; 14:18426. [PMID: 39117696 PMCID: PMC11310328 DOI: 10.1038/s41598-024-66600-1] [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: 10/27/2023] [Accepted: 07/02/2024] [Indexed: 08/10/2024] Open
Abstract
High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software programs for image analysis workflows typically do not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, nucleus registration, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new analysis modules for existing analysis pipelines and to adding new analysis modules. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI software platform for a variety of cell biology applications.
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Affiliation(s)
- Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Christopher H Bohrer
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Nadezda A Fursova
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Krishnendu Guin
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Varun Sood
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Daniel R Larson
- System Biology of Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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16
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Goyzueta-Mamani LD, Barazorda-Ccahuana HL, Candia-Puma MA, Galdino AS, Machado-de-Avila RA, Giunchetti RC, Medina-Franco JL, Florin-Christensen M, Ferraz Coelho EA, Chávez-Fumagalli MA. Targeting Leishmania infantum Mannosyl-oligosaccharide glucosidase with natural products: potential pH-dependent inhibition explored through computer-aided drug design. Front Pharmacol 2024; 15:1403203. [PMID: 38873424 PMCID: PMC11169604 DOI: 10.3389/fphar.2024.1403203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/25/2024] [Indexed: 06/15/2024] Open
Abstract
Visceral Leishmaniasis (VL) is a serious public health issue, documented in more than ninety countries, where an estimated 500,000 new cases emerge each year. Regardless of novel methodologies, advancements, and experimental interventions, therapeutic limitations, and drug resistance are still challenging. For this reason, based on previous research, we screened natural products (NP) from Nuclei of Bioassays, Ecophysiology, and Biosynthesis of Natural Products Database (NuBBEDB), Mexican Compound Database of Natural Products (BIOFACQUIM), and Peruvian Natural Products Database (PeruNPDB) databases, in addition to structural analogs of Miglitol and Acarbose, which have been suggested as treatments for VL and have shown encouraging action against parasite's N-glycan biosynthesis. Using computer-aided drug design (CADD) approaches, the potential inhibitory effect of these NP candidates was evaluated by inhibiting the Mannosyl-oligosaccharide Glucosidase Protein (MOGS) from Leishmania infantum, an enzyme essential for the protein glycosylation process, at various pH to mimic the parasite's changing environment. Also, computational analysis was used to evaluate the Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) profile, while molecular dynamic simulations were used to gather information on the interactions between these ligands and the protein target. Our findings indicated that Ocotillone and Subsessiline have potential antileishmanial effects at pH 5 and 7, respectively, due to their high binding affinity to MOGS and interactions in the active center. Furthermore, these compounds were non-toxic and had the potential to be administered orally. This research indicates the promising anti-leishmanial activity of Ocotillone and Subsessiline, suggesting further validation through in vitro and in vivo experiments.
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Affiliation(s)
- Luis Daniel Goyzueta-Mamani
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
| | - Haruna Luz Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
| | - Mayron Antonio Candia-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa, Peru
| | | | | | - Rodolfo Cordeiro Giunchetti
- Laboratório de Biologia das Interações Celulares, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais (INCT-DT), Salvador, Brazil
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mónica Florin-Christensen
- Instituto de Patobiología Veterinaria, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Patologia Clínica, Colégio Técnico da Universidade Federal de Minas Gerais (COLTEC), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
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17
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Long TZ, Jiang DJ, Shi SH, Deng YC, Wang WX, Cao DS. Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence. J Chem Inf Model 2024; 64:3222-3236. [PMID: 38498003 DOI: 10.1021/acs.jcim.4c00159] [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: 03/19/2024]
Abstract
Liver microsomal stability, a crucial aspect of metabolic stability, significantly impacts practical drug discovery. However, current models for predicting liver microsomal stability are based on limited molecular information from a single species. To address this limitation, we constructed the largest public database of compounds from three common species: human, rat, and mouse. Subsequently, we developed a series of classification models using both traditional descriptor-based and classic graph-based machine learning (ML) algorithms. Remarkably, the best-performing models for the three species achieved Matthews correlation coefficients (MCCs) of 0.616, 0.603, and 0.574, respectively, on the test set. Furthermore, through the construction of consensus models based on these individual models, we have demonstrated their superior predictive performance in comparison with the existing models of the same type. To explore the similarities and differences in the properties of liver microsomal stability among multispecies molecules, we conducted preliminary interpretative explorations using the Shapley additive explanations (SHAP) and atom heatmap approaches for the models and misclassified molecules. Additionally, we further investigated representative structural modifications and substructures that decrease the liver microsomal stability in different species using the matched molecule pair analysis (MMPA) method and substructure extraction techniques. The established prediction models, along with insightful interpretation information regarding liver microsomal stability, will significantly contribute to enhancing the efficiency of exploring practical drugs for development.
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Affiliation(s)
- Teng-Zhi Long
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - De-Jun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Shao-Hua Shi
- Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR 999077, P. R. China
| | - You-Chao Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
- Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR 999077, P. R. China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
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18
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von Lersner A, Fernandes F, Ozawa PM, Jackson M, Masureel M, Ho H, Lima SM, Vagner T, Sung BH, Wehbe M, Franze K, Pua H, Wilson JT, Irish JM, Weaver AM, Di Vizio D, Zijlstra A. Multiparametric Single-Vesicle Flow Cytometry Resolves Extracellular Vesicle Heterogeneity and Reveals Selective Regulation of Biogenesis and Cargo Distribution. ACS NANO 2024; 18:10464-10484. [PMID: 38578701 PMCID: PMC11025123 DOI: 10.1021/acsnano.3c11561] [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: 11/20/2023] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Mammalian cells release a heterogeneous array of extracellular vesicles (EVs) that contribute to intercellular communication by means of the cargo that they carry. To resolve EV heterogeneity and determine if cargo is partitioned into select EV populations, we developed a method named "EV Fingerprinting" that discerns distinct vesicle populations using dimensional reduction of multiparametric data collected by quantitative single-EV flow cytometry. EV populations were found to be discernible by a combination of membrane order and EV size, both of which were obtained through multiparametric analysis of fluorescent features from the lipophilic dye Di-8-ANEPPS incorporated into the lipid bilayer. Molecular perturbation of EV secretion and biogenesis through respective ablation of the small GTPase Rab27a and overexpression of the EV-associated tetraspanin CD63 revealed distinct and selective alterations in EV populations, as well as cargo distribution. While Rab27a disproportionately affects all small EV populations with high membrane order, the overexpression of CD63 selectively increased the production of one small EV population of intermediate membrane order. Multiplexing experiments subsequently revealed that EV cargos have a distinct, nonrandom distribution with CD63 and CD81 selectively partitioning into smaller vs larger EVs, respectively. These studies not only present a method to probe EV biogenesis but also reveal how the selective partitioning of cargo contributes to EV heterogeneity.
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Affiliation(s)
- Ariana
K. von Lersner
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
| | - Fabiane Fernandes
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Institute
of Applied Biosciences and Chemistry, Hogeschool
Arnhem en Nijmegen University of Applied Sciences, Nijmegen 6525 EM, Gelderland, Netherlands
| | - Patricia Midori
Murobushi Ozawa
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Marques Jackson
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
| | - Matthieu Masureel
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Hoangdung Ho
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Sierra M. Lima
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Tatyana Vagner
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Bong Hwan Sung
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Mohamed Wehbe
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kai Franze
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
- KNIME
GmbH, Konstanz 78467, Germany
| | - Heather Pua
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - John T. Wilson
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jonathan M. Irish
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Alissa M. Weaver
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Dolores Di Vizio
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Andries Zijlstra
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
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19
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Mansouri K, Moreira-Filho JT, Lowe CN, Charest N, Martin T, Tkachenko V, Judson R, Conway M, Kleinstreuer NC, Williams AJ. Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling. J Cheminform 2024; 16:19. [PMID: 38378618 PMCID: PMC10880251 DOI: 10.1186/s13321-024-00814-3] [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: 11/29/2023] [Accepted: 02/10/2024] [Indexed: 02/22/2024] Open
Abstract
The rapid increase of publicly available chemical structures and associated experimental data presents a valuable opportunity to build robust QSAR models for applications in different fields. However, the common concern is the quality of both the chemical structure information and associated experimental data. This is especially true when those data are collected from multiple sources as chemical substance mappings can contain many duplicate structures and molecular inconsistencies. Such issues can impact the resulting molecular descriptors and their mappings to experimental data and, subsequently, the quality of the derived models in terms of accuracy, repeatability, and reliability. Herein we describe the development of an automated workflow to standardize chemical structures according to a set of standard rules and generate two and/or three-dimensional "QSAR-ready" forms prior to the calculation of molecular descriptors. The workflow was designed in the KNIME workflow environment and consists of three high-level steps. First, a structure encoding is read, and then the resulting in-memory representation is cross-referenced with any existing identifiers for consistency. Finally, the structure is standardized using a series of operations including desalting, stripping of stereochemistry (for two-dimensional structures), standardization of tautomers and nitro groups, valence correction, neutralization when possible, and then removal of duplicates. This workflow was initially developed to support collaborative modeling QSAR projects to ensure consistency of the results from the different participants. It was then updated and generalized for other modeling applications. This included modification of the "QSAR-ready" workflow to generate "MS-ready structures" to support the generation of substance mappings and searches for software applications related to non-targeted analysis mass spectrometry. Both QSAR and MS-ready workflows are freely available in KNIME, via standalone versions on GitHub, and as docker container resources for the scientific community. Scientific contribution: This work pioneers an automated workflow in KNIME, systematically standardizing chemical structures to ensure their readiness for QSAR modeling and broader scientific applications. By addressing data quality concerns through desalting, stereochemistry stripping, and normalization, it optimizes molecular descriptors' accuracy and reliability. The freely available resources in KNIME, GitHub, and docker containers democratize access, benefiting collaborative research and advancing diverse modeling endeavors in chemistry and mass spectrometry.
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Affiliation(s)
- Kamel Mansouri
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
| | - José T Moreira-Filho
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Charles N Lowe
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Nathaniel Charest
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Todd Martin
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | | | - Richard Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Mike Conway
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Nicole C Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Antony J Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
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20
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Barazorda-Ccahuana HL, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Galdino AS, Machado-de-Ávila RA, Giunchetti RC, Coelho EAF, Chávez-Fumagalli MA. Targeting with Structural Analogs of Natural Products the Purine Salvage Pathway in Leishmania (Leishmania) infantum by Computer-Aided Drug-Design Approaches. Trop Med Infect Dis 2024; 9:41. [PMID: 38393130 PMCID: PMC10891554 DOI: 10.3390/tropicalmed9020041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Visceral Leishmaniasis (VL) has a high death rate, with 500,000 new cases and 50,000 deaths occurring annually. Despite the development of novel strategies and technologies, there is no adequate treatment for the disease. Therefore, the purpose of this study is to find structural analogs of natural products as potential novel drugs to treat VL. We selected structural analogs from natural products that have shown antileishmanial activities, and that may impede the purine salvage pathway using computer-aided drug-design (CADD) approaches. For these, we started with the vastly studied target in the pathway, the adenine phosphoribosyl transferase (APRT) protein, which alone is non-essential for the survival of the parasite. Keeping this in mind, we search for a substance that can bind to multiple targets throughout the pathway. Computational techniques were used to study the purine salvage pathway from Leishmania infantum, and molecular dynamic simulations were used to gather information on the interactions between ligands and proteins. Because of its low homology to human proteins and its essential role in the purine salvage pathway proteins network interaction, the findings further highlight the significance of adenylosuccinate lyase protein (ADL) as a therapeutic target. An analog of the alkaloid Skimmianine, N,N-diethyl-4-methoxy-1-benzofuran-6-carboxamide, demonstrated a good binding affinity to APRT and ADL targets, no expected toxicity, and potential for oral route administration. This study indicates that the compound may have antileishmanial activity, which was granted in vitro and in vivo experiments to settle this finding in the future.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Alexsandro Sobreira Galdino
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal São João Del-Rei, Divinópolis 35501-296, MG, Brazil
| | | | - Rodolfo Cordeiro Giunchetti
- Laboratório de Biologia das Interações Celulares, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, INCT-DT, Salvador 40015-970, BA, Brazil
| | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
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21
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Jan M, Spangaro A, Lenartowicz M, Mattiazzi Usaj M. From pixels to insights: Machine learning and deep learning for bioimage analysis. Bioessays 2024; 46:e2300114. [PMID: 38058114 DOI: 10.1002/bies.202300114] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023]
Abstract
Bioimage analysis plays a critical role in extracting information from biological images, enabling deeper insights into cellular structures and processes. The integration of machine learning and deep learning techniques has revolutionized the field, enabling the automated, reproducible, and accurate analysis of biological images. Here, we provide an overview of the history and principles of machine learning and deep learning in the context of bioimage analysis. We discuss the essential steps of the bioimage analysis workflow, emphasizing how machine learning and deep learning have improved preprocessing, segmentation, feature extraction, object tracking, and classification. We provide examples that showcase the application of machine learning and deep learning in bioimage analysis. We examine user-friendly software and tools that enable biologists to leverage these techniques without extensive computational expertise. This review is a resource for researchers seeking to incorporate machine learning and deep learning in their bioimage analysis workflows and enhance their research in this rapidly evolving field.
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Affiliation(s)
- Mahta Jan
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Allie Spangaro
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Michelle Lenartowicz
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
| | - Mojca Mattiazzi Usaj
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Canada
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22
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Gogoberidze N, Cimini BA. Defining the boundaries: challenges and advances in identifying cells in microscopy images. Curr Opin Biotechnol 2024; 85:103055. [PMID: 38142646 PMCID: PMC11170924 DOI: 10.1016/j.copbio.2023.103055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/26/2023]
Abstract
Segmentation, or the outlining of objects within images, is a critical step in the measurement and analysis of cells within microscopy images. While improvements continue to be made in tools that rely on classical methods for segmentation, deep learning-based tools increasingly dominate advances in the technology. Specialist models such as Cellpose continue to improve in accuracy and user-friendliness, and segmentation challenges such as the Multi-Modality Cell Segmentation Challenge continue to push innovation in accuracy across widely varying test data as well as efficiency and usability. Increased attention on documentation, sharing, and evaluation standards is leading to increased user-friendliness and acceleration toward the goal of a truly universal method.
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Affiliation(s)
| | - Beth A Cimini
- Imaging Platform, Broad Institute, Cambridge, MA 02142, USA.
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23
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Mikutis S, Lawrinowitz S, Kretzer C, Dunsmore L, Sketeris L, Rodrigues T, Werz O, Bernardes GJL. Machine Learning Uncovers Natural Product Modulators of the 5-Lipoxygenase Pathway and Facilitates the Elucidation of Their Biological Mechanisms. ACS Chem Biol 2024; 19:217-229. [PMID: 38149598 PMCID: PMC10804367 DOI: 10.1021/acschembio.3c00725] [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: 11/28/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Machine learning (ML) models have made inroads into chemical sciences, with optimization of chemical reactions and prediction of biologically active molecules being prime examples thereof. These models excel where physical experiments are expensive or time-consuming, for example, due to large scales or the need for materials that are difficult to obtain. Studies of natural products suffer from these issues─this class of small molecules is known for its wealth of structural diversity and wide-ranging biological activities, but their investigation is hindered by poor synthetic accessibility and lack of scalability. To facilitate the evaluation of these molecules, we designed ML models that predict which natural products can interact with a particular target or a relevant pathway. Here, we focused on discovering natural products that are capable of modulating the 5-lipoxygenase (5-LO) pathway that plays key roles in lipid signaling and inflammation. These computational approaches led to the identification of nine natural products that either directly inhibit the activity of the 5-LO enzyme or affect the cellular 5-LO pathway. Further investigation of one of these molecules, deltonin, led us to discover a new cell-type-selective mechanism of action. Our ML approach helped deorphanize natural products as well as shed light on their mechanisms and can be broadly applied to other use cases in chemical biology.
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Affiliation(s)
- Sigitas Mikutis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Stefanie Lawrinowitz
- Department
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Christian Kretzer
- Department
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Lavinia Dunsmore
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Laurynas Sketeris
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Tiago Rodrigues
- Instituto
de Investigação do Medicamento (iMed), Faculdade de
Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Oliver Werz
- Department
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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24
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Zhan C, Tang T, Wu E, Zhang Y, He M, Wu R, Bi C, Wang J, Zhang Y, Shen B. From multi-omics approaches to personalized medicine in myocardial infarction. Front Cardiovasc Med 2023; 10:1250340. [PMID: 37965091 PMCID: PMC10642346 DOI: 10.3389/fcvm.2023.1250340] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Myocardial infarction (MI) is a prevalent cardiovascular disease characterized by myocardial necrosis resulting from coronary artery ischemia and hypoxia, which can lead to severe complications such as arrhythmia, cardiac rupture, heart failure, and sudden death. Despite being a research hotspot, the etiological mechanism of MI remains unclear. The emergence and widespread use of omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and other omics, have provided new opportunities for exploring the molecular mechanism of MI and identifying a large number of disease biomarkers. However, a single-omics approach has limitations in understanding the complex biological pathways of diseases. The multi-omics approach can reveal the interaction network among molecules at various levels and overcome the limitations of the single-omics approaches. This review focuses on the omics studies of MI, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and other omics. The exploration extended into the domain of multi-omics integrative analysis, accompanied by a compilation of diverse online resources, databases, and tools conducive to these investigations. Additionally, we discussed the role and prospects of multi-omics approaches in personalized medicine, highlighting the potential for improving diagnosis, treatment, and prognosis of MI.
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Affiliation(s)
- Chaoying Zhan
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tong Tang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Erman Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxin Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengqiao He
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Rongrong Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Bi
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiao Wang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yingbo Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bairong Shen
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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25
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Donisi L, Jacob D, Guerrini L, Prisco G, Esposito F, Cesarelli M, Amato F, Gargiulo P. sEMG Spectral Analysis and Machine Learning Algorithms Are Able to Discriminate Biomechanical Risk Classes Associated with Manual Material Liftings. Bioengineering (Basel) 2023; 10:1103. [PMID: 37760205 PMCID: PMC10525808 DOI: 10.3390/bioengineering10091103] [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: 07/24/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Manual material handling and load lifting are activities that can cause work-related musculoskeletal disorders. For this reason, the National Institute for Occupational Safety and Health proposed an equation depending on the following parameters: intensity, duration, frequency, and geometric characteristics associated with the load lifting. In this paper, we explore the feasibility of several Machine Learning (ML) algorithms, fed with frequency-domain features extracted from electromyographic (EMG) signals of back muscles, to discriminate biomechanical risk classes defined by the Revised NIOSH Lifting Equation. The EMG signals of the multifidus and erector spinae muscles were acquired by means of a wearable device for surface EMG and then segmented to extract several frequency-domain features relating to the Total Power Spectrum of the EMG signal. These features were fed to several ML algorithms to assess their prediction power. The ML algorithms produced interesting results in the classification task, with the Support Vector Machine algorithm outperforming the others with accuracy and Area under the Receiver Operating Characteristic Curve values of up to 0.985. Moreover, a correlation between muscular fatigue and risky lifting activities was found. These results showed the feasibility of the proposed methodology-based on wearable sensors and artificial intelligence-to predict the biomechanical risk associated with load lifting. A future investigation on an enriched study population and additional lifting scenarios could confirm the potential of the proposed methodology and its applicability in the field of occupational ergonomics.
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Affiliation(s)
- Leandro Donisi
- Department of Advanced Medical and Surgical Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
- The Institute of Biomedical and Neural Engineering, School of Science and Engineering, Reykjavik University, 102 Reykjavik, Iceland; (D.J.); (L.G.); (P.G.)
| | - Deborah Jacob
- The Institute of Biomedical and Neural Engineering, School of Science and Engineering, Reykjavik University, 102 Reykjavik, Iceland; (D.J.); (L.G.); (P.G.)
| | - Lorena Guerrini
- The Institute of Biomedical and Neural Engineering, School of Science and Engineering, Reykjavik University, 102 Reykjavik, Iceland; (D.J.); (L.G.); (P.G.)
- Department of Engineering, University of Campania Luigi Vanvitelli, 81031 Aversa, Italy
| | - Giuseppe Prisco
- Department of Medicine and Health Sciences, University of Molise, 86100 Campobasso, Italy;
| | - Fabrizio Esposito
- Department of Advanced Medical and Surgical Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy;
| | - Mario Cesarelli
- Department of Engineering, University of Sannio, 82100 Benevento, Italy;
| | - Francesco Amato
- Department of Information Technology and Electrical Engineering, University of Naples Federico II, 80125 Naples, Italy;
| | - Paolo Gargiulo
- The Institute of Biomedical and Neural Engineering, School of Science and Engineering, Reykjavik University, 102 Reykjavik, Iceland; (D.J.); (L.G.); (P.G.)
- Department of Science, Landspitali University Hospital, 102 Reykjavik, Iceland
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26
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Barazorda-Ccahuana HL, Ranilla LG, Candia-Puma MA, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Davila-Del-Carpio G, Medina-Franco JL, Chávez-Fumagalli MA. PeruNPDB: the Peruvian Natural Products Database for in silico drug screening. Sci Rep 2023; 13:7577. [PMID: 37165197 PMCID: PMC10170056 DOI: 10.1038/s41598-023-34729-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023] Open
Abstract
Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discovery development. For this reason, several countries such as Mexico, Brazil, India, and China have initiatives to assemble and maintain NPs databases that are representative of their diversity and ethnopharmacological usage. We describe the assembly, curation, and chemoinformatic evaluation of the content and coverage in chemical space, as well as the physicochemical attributes and chemical diversity of the initial version of the Peruvian Natural Products Database (PeruNPDB), which contains 280 natural products. Access to PeruNPDB is available for free ( https://perunpdb.com.pe/ ). The PeruNPDB's collection is intended to be used in a variety of tasks, such as virtual screening campaigns against various disease targets or biological endpoints. This emphasizes the significance of biodiversity protection both directly and indirectly on human health.
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Affiliation(s)
- Haruna L Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Lena Gálvez Ranilla
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
- Escuela Profesional de Ingeniería de Industria Alimentaria, Facultad de Ciencias e Ingenierías Biológicas y Químicas, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
| | - Mayron Antonio Candia-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Gonzalo Davila-Del-Carpio
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru.
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27
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Lei Y, Chen X, Shi J, Liu Y, Xu YJ. Development and application of a data processing method for food metabolomics analysis. Mol Omics 2023. [PMID: 37139637 DOI: 10.1039/d2mo00338d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Food metabolomics is described as the implementation of metabolomics to food systems such as food materials, food processing, and food nutrition. These applications generally create large amounts of data, and although technologies exist to analyze these data and different tools exist for various ecosystems, downstream analysis is still a challenge and the tools are not integrated into a single method. In this article, we developed a data processing method for untargeted LC-MS data in metabolomics, derived from the integration of computational MS tools from OpenMS into the workflow system Konstanz Information Miner (KNIME). This method can analyze raw MS data and produce high-quality visualization. A MS1 spectra-based identification, two MS2 spectra-based identification workflows and a GNPSExport-GNPS workflow are included in this method. Compared with conventional approaches, the results of MS1&MS2 spectra-based identification workflows are combined in this approach via the tolerance of retention times and mass to charge ratios (m/z), which can greatly reduce the rate of false positives in metabolomics datasets. In our example, filtering with the tolerance removed more than 50% of the possible identifications while retaining 90% of the correct identification. The results demonstrated that the developed method is a rapid and reliable method for food metabolomics data processing.
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Affiliation(s)
- Yuanluo Lei
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Xiaoying Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
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28
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Romero S, Unchwaniwala N, Evans EL, Eliceiri KW, Loeb DD, Sherer NM. Live Cell Imaging Reveals HBV Capsid Translocation from the Nucleus To the Cytoplasm Enabled by Cell Division. mBio 2023; 14:e0330322. [PMID: 36809075 PMCID: PMC10127671 DOI: 10.1128/mbio.03303-22] [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: 11/29/2022] [Accepted: 01/17/2023] [Indexed: 02/23/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly is traditionally thought to occur predominantly in the cytoplasm, where the virus gains access to the virion egress pathway. To better define sites of HBV capsid assembly, we carried out single cell imaging of HBV Core protein (Cp) subcellular trafficking over time under conditions supporting genome packaging and reverse transcription in Huh7 hepatocellular carcinoma cells. Time-course analyses including live cell imaging of fluorescently tagged Cp derivatives showed Cp to accumulate in the nucleus at early time points (~24 h), followed by a marked re-distribution to the cytoplasm at 48 to 72 h. Nucleus-associated Cp was confirmed to be capsid and/or high-order assemblages using a novel dual label immunofluorescence strategy. Nuclear-to-cytoplasmic re-localization of Cp occurred predominantly during nuclear envelope breakdown in conjunction with cell division, followed by strong cytoplasmic retention of Cp. Blocking cell division resulted in strong nuclear entrapment of high-order assemblages. A Cp mutant, Cp-V124W, predicted to exhibit enhanced assembly kinetics, also first trafficked to the nucleus to accumulate at nucleoli, consistent with the hypothesis that Cp's transit to the nucleus is a strong and constitutive process. Taken together, these results provide support for the nucleus as an early-stage site of HBV capsid assembly, and provide the first dynamic evidence of cytoplasmic retention after cell division as a mechanism underpinning capsid nucleus-to-cytoplasm relocalization. IMPORTANCE Hepatitis B virus (HBV) is an enveloped, reverse-transcribing DNA virus that is a major cause of liver disease and hepatocellular carcinoma. Subcellular trafficking events underpinning HBV capsid assembly and virion egress remain poorly characterized. Here, we developed a combination of fixed and long-term (>24 h) live cell imaging technologies to study the single cell trafficking dynamics of the HBV Core Protein (Cp). We demonstrate that Cp first accumulates in the nucleus, and forms high-order structures consistent with capsids, with the predominant route of nuclear egress being relocalization to the cytoplasm during cell division in conjunction with nuclear membrane breakdown. Single cell video microscopy demonstrated unequivocally that Cp's localization to the nucleus is constitutive. This study represents a pioneering application of live cell imaging to study HBV subcellular transport, and demonstrates links between HBV Cp and the cell cycle.
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Affiliation(s)
- Sofia Romero
- McArdle Laboratory for Cancer Research (Department of Oncology), University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Nuruddin Unchwaniwala
- McArdle Laboratory for Cancer Research (Department of Oncology), University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Edward L. Evans
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Daniel D. Loeb
- McArdle Laboratory for Cancer Research (Department of Oncology), University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research (Department of Oncology), University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin, USA
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29
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Lignieres L, Sénécaut N, Dang T, Bellutti L, Hamon M, Terrier S, Legros V, Chevreux G, Lelandais G, Mège RM, Dumont J, Camadro JM. Extending the Range of SLIM-Labeling Applications: From Human Cell Lines in Culture to Caenorhabditis elegans Whole-Organism Labeling. J Proteome Res 2023; 22:996-1002. [PMID: 36748112 PMCID: PMC9990122 DOI: 10.1021/acs.jproteome.2c00699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The simple light isotope metabolic-labeling technique relies on the in vivo biosynthesis of amino acids from U-[12C]-labeled molecules provided as the sole carbon source. The incorporation of the resulting U-[12C]-amino acids into proteins presents several key advantages for mass-spectrometry-based proteomics analysis, as it results in more intense monoisotopic ions, with a better signal-to-noise ratio in bottom-up analysis. In our initial studies, we developed the simple light isotope metabolic (SLIM)-labeling strategy using prototrophic eukaryotic microorganisms, the yeasts Candida albicans and Saccharomyces cerevisiae, as well as strains with genetic markers that lead to amino-acid auxotrophy. To extend the range of SLIM-labeling applications, we evaluated (i) the incorporation of U-[12C]-glucose into proteins of human cells grown in a complex RPMI-based medium containing the labeled molecule, considering that human cell lines require a large number of essential amino-acids to support their growth, and (ii) an indirect labeling strategy in which the nematode Caenorhabditis elegans grown on plates was fed U-[12C]-labeled bacteria (Escherichia coli) and the worm proteome analyzed for 12C incorporation into proteins. In both cases, we were able to demonstrate efficient incorporation of 12C into the newly synthesized proteins, opening the way for original approaches in quantitative proteomics.
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Affiliation(s)
- Laurent Lignieres
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Nicolas Sénécaut
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Tien Dang
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Laura Bellutti
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Marion Hamon
- Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Samuel Terrier
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Véronique Legros
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Gaëlle Lelandais
- Institut de Biologie Intégrative de la Cellule, F-91190 Gif-sur-Yvette, France
| | - René-Marc Mège
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Julien Dumont
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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30
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Zhao Y, Cao LY, Zhao YX, Wang F, Xie LL, Xing HY, Wang Q. Medical record data-enabled machine learning can enhance prediction of left atrial appendage thrombosis in nonvalvular atrial fibrillation. Thromb Res 2023; 223:174-183. [PMID: 36764084 DOI: 10.1016/j.thromres.2023.01.001] [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: 10/11/2022] [Revised: 11/16/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
BACKGROUND As a major complication of non-valvular atrial fibrillation (NVAF), left atrial appendage (LAA) thrombosis is associated with cerebral ischemic strokes, as well as high morbidity. Due to insufficient incorporation of risk factors, most current scoring methods are limited to the analysis of relationships between clinical characteristics and LAA thrombosis rather than detecting potential risk. Therefore, this study proposes a clinical data-driven machine learning method to predict LAA thrombosis of NVAF. METHODS Patients with NVAF from January 2014 to June 2022 were enrolled from Southwest Hospital. We selected 40 variables for analysis, including demographic data, medical history records, laboratory results, and the structure of LAA. Three machine learning algorithms were adopted to construct classifiers for the prediction of LAA thrombosis risk. The most important variables related to LAA thrombosis and their influences were recognized by SHapley Addictive exPlanations method. In addition, we compared our model with CHADS2 and CHADS2-VASc scoring methods. RESULTS A total of 713 participants were recruited, including 127 patients with LAA thrombosis and 586 patients with no obvious thrombosis. The consensus models based on Random Forest and eXtreme Gradient Boosting LAA thrombosis prediction (RXTP) achieved the best accuracy of 0.865, significantly outperforming CHADS2 score and CHA2DS2-VASc score (0.757 and 0.754, respectively). The SHAP results showed that B-type natriuretic peptide, left atrial appendage width, C-reactive protein, Fibrinogen and estimated glomerular filtration rate are closely related to the risk of LAA thrombosis in nonvalvular atrial fibrillation. CONCLUSIONS The RXTP-NVAF model is the most effective model with the greatest ROC value and recall rate. The summarized risk factors obtained from SHAP enable the optimization of the treatment strategy, thereby preventing thromboembolism events and the occurrence of cardiogenic ischemic stroke.
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Affiliation(s)
- Yue Zhao
- Department of Pharmacy, the First Affiliated Hospital of Army Medical University (Third Military Medical University),Chongqing, China
| | - Li-Ya Cao
- Department of Pharmacy, the First Affiliated Hospital of Army Medical University (Third Military Medical University),Chongqing, China
| | - Ying-Xin Zhao
- Department of Pharmacy, Army Medical Center, Army Medical University (Third Military Medical University),Chongqing, China
| | - Fei Wang
- Medical Big Data and Artificial Intelligence Center, the First Affiliated Hospital of Army Medical University (Third Military Medical University), Chongqing, China
| | - Lin-Li Xie
- Department of Pharmacy, the First Affiliated Hospital of Army Medical University (Third Military Medical University),Chongqing, China
| | - Hai-Yan Xing
- Department of Pharmacy, Army Medical Center, Army Medical University (Third Military Medical University),Chongqing, China.
| | - Qian Wang
- Department of Pharmacy, the First Affiliated Hospital of Army Medical University (Third Military Medical University),Chongqing, China.
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Su Y, Huang C, Yin W, Lyu X, Ma L, Tao Z. Diabetes Mellitus risk prediction using age adaptation models. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2022.104381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Long TZ, Shi SH, Liu S, Lu AP, Liu ZQ, Li M, Hou TJ, Cao DS. Structural Analysis and Prediction of Hematotoxicity Using Deep Learning Approaches. J Chem Inf Model 2023; 63:111-125. [PMID: 36472475 DOI: 10.1021/acs.jcim.2c01088] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hematotoxicity has been becoming a serious but overlooked toxicity in drug discovery. However, only a few in silico models have been reported for the prediction of hematotoxicity. In this study, we constructed a high-quality dataset comprising 759 hematotoxic compounds and 1623 nonhematotoxic compounds and then established a series of classification models based on a combination of seven machine learning (ML) algorithms and nine molecular representations. The results based on two data partitioning strategies and applicability domain (AD) analysis illustrate that the best prediction model based on Attentive FP yielded a balanced accuracy (BA) of 72.6%, an area under the receiver operating characteristic curve (AUC) value of 76.8% for the validation set, and a BA of 69.2%, an AUC of 75.9% for the test set. In addition, compared with existing filtering rules and models, our model achieved the highest BA value of 67.5% for the external validation set. Additionally, the shapley additive explanation (SHAP) and atom heatmap approaches were utilized to discover the important features and structural fragments related to hematotoxicity, which could offer helpful tips to detect undesired positive substances. Furthermore, matched molecular pair analysis (MMPA) and representative substructure derivation technique were employed to further characterize and investigate the transformation principles and distinctive structural features of hematotoxic chemicals. We believe that the novel graph-based deep learning algorithms and insightful interpretation presented in this study can be used as a trustworthy and effective tool to assess hematotoxicity in the development of new drugs.
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Affiliation(s)
- Teng-Zhi Long
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Shao-Hua Shi
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China.,Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, 0000, P. R. China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Ai-Ping Lu
- Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, 0000, P. R. China
| | - Zhao-Qian Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha 410083, P. R. China
| | - Ting-Jun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China.,Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, 0000, P. R. China.,Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
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Griess K, Rieck M, Müller N, Karsai G, Hartwig S, Pelligra A, Hardt R, Schlegel C, Kuboth J, Uhlemeyer C, Trenkamp S, Jeruschke K, Weiss J, Peifer-Weiss L, Xu W, Cames S, Yi X, Cnop M, Beller M, Stark H, Kondadi AK, Reichert AS, Markgraf D, Wammers M, Häussinger D, Kuss O, Lehr S, Eizirik D, Lickert H, Lammert E, Roden M, Winter D, Al-Hasani H, Höglinger D, Hornemann T, Brüning JC, Belgardt BF. Sphingolipid subtypes differentially control proinsulin processing and systemic glucose homeostasis. Nat Cell Biol 2023; 25:20-29. [PMID: 36543979 PMCID: PMC9859757 DOI: 10.1038/s41556-022-01027-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 10/11/2022] [Indexed: 12/24/2022]
Abstract
Impaired proinsulin-to-insulin processing in pancreatic β-cells is a key defective step in both type 1 diabetes and type 2 diabetes (T2D) (refs. 1,2), but the mechanisms involved remain to be defined. Altered metabolism of sphingolipids (SLs) has been linked to development of obesity, type 1 diabetes and T2D (refs. 3-8); nonetheless, the role of specific SL species in β-cell function and demise is unclear. Here we define the lipid signature of T2D-associated β-cell failure, including an imbalance of specific very-long-chain SLs and long-chain SLs. β-cell-specific ablation of CerS2, the enzyme necessary for generation of very-long-chain SLs, selectively reduces insulin content, impairs insulin secretion and disturbs systemic glucose tolerance in multiple complementary models. In contrast, ablation of long-chain-SL-synthesizing enzymes has no effect on insulin content. By quantitatively defining the SL-protein interactome, we reveal that CerS2 ablation affects SL binding to several endoplasmic reticulum-Golgi transport proteins, including Tmed2, which we define as an endogenous regulator of the essential proinsulin processing enzyme Pcsk1. Our study uncovers roles for specific SL subtypes and SL-binding proteins in β-cell function and T2D-associated β-cell failure.
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Affiliation(s)
- Kerstin Griess
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Michael Rieck
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Nadine Müller
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Gergely Karsai
- Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland
- Institute for Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Sonja Hartwig
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Angela Pelligra
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Robert Hardt
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University Bonn, Bonn, Germany
| | - Caroline Schlegel
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Jennifer Kuboth
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Celina Uhlemeyer
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Sandra Trenkamp
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kay Jeruschke
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jürgen Weiss
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Leon Peifer-Weiss
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Weiwei Xu
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Sandra Cames
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Xiaoyan Yi
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels, Belgium
| | - Miriam Cnop
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels, Belgium
- Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Mathias Beller
- Institute for Mathematical Modeling of Biological Systems and Systems Biology of Lipid Metabolism, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Arun Kumar Kondadi
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Markgraf
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marianne Wammers
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology and Infectious Diseases, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver Kuss
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Centre for Health and Society, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefan Lehr
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Decio Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Heiko Lickert
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, Neuherberg, Germany
- Department of Medicine, Technical University of Munich, Munich, Germany
| | - Eckhard Lammert
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Metabolic Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Roden
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University Bonn, Bonn, Germany
| | - Hadi Al-Hasani
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Doris Höglinger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Thorsten Hornemann
- Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland
- Institute for Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Jens C Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
- Policlinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany
- Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Bengt-Frederik Belgardt
- Institute for Vascular and Islet Cell Biology, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
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Sharma C, Sakhuja S, Nijjer S. Recent trends of green human resource management: Text mining and network analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:84916-84935. [PMID: 35790632 PMCID: PMC9255839 DOI: 10.1007/s11356-022-21471-9] [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: 08/13/2021] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Issues of the environmental crisis are being addressed by researchers, government, and organizations alike. GHRM is one such field that is receiving lots of research focus since it is targeted at greening the firms and making them eco-friendly. This research reviews 317 articles from the Scopus database published on green human resource management (GHRM) from 2008 to 2021. The study applies text mining, latent semantic analysis (LSA), and network analysis to explore the trends in the research field in GHRM and establish the relationship between the quantitative and qualitative literature of GHRM. The study has been carried out using KNIME and VOSviewer tools. As a result, the research identifies five recent research trends in GHRM using K-mean clustering. Future researchers can work upon these identified trends to solve environmental issues, make the environment eco-friendly, and motivate firms to implement GHRM in their practices.
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Affiliation(s)
| | - Sumit Sakhuja
- Chitkara Business School, Chitkara University, Rajpura, Punjab India
| | - Shivinder Nijjer
- Chitkara Business School, Chitkara University, Rajpura, Punjab India
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Abstract
Applying computational statistics or machine learning methods to data is a key component of many scientific studies, in any field, but alone might not be sufficient to generate robust and reliable outcomes and results. Before applying any discovery method, preprocessing steps are necessary to prepare the data to the computational analysis. In this framework, data cleaning and feature engineering are key pillars of any scientific study involving data analysis and that should be adequately designed and performed since the first phases of the project. We call "feature" a variable describing a particular trait of a person or an observation, recorded usually as a column in a dataset. Even if pivotal, these data cleaning and feature engineering steps sometimes are done poorly or inefficiently, especially by beginners and unexperienced researchers. For this reason, we propose here our quick tips for data cleaning and feature engineering on how to carry out these important preprocessing steps correctly avoiding common mistakes and pitfalls. Although we designed these guidelines with bioinformatics and health informatics scenarios in mind, we believe they can more in general be applied to any scientific area. We therefore target these guidelines to any researcher or practitioners wanting to perform data cleaning or feature engineering. We believe our simple recommendations can help researchers and scholars perform better computational analyses that can lead, in turn, to more solid outcomes and more reliable discoveries.
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Affiliation(s)
- Davide Chicco
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Luca Oneto
- Dipartimento di Informatica Bioingegneria Robotica e Ingegneria dei Sistemi, Università di Genova, Genoa, Italy
- ZenaByte S.r.l., Genoa, Italy
| | - Erica Tavazzi
- Dipartimento di Ingegneria dell’Informazione, Università di Padova, Padua, Italy
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Morger A, Garcia de Lomana M, Norinder U, Svensson F, Kirchmair J, Mathea M, Volkamer A. Studying and mitigating the effects of data drifts on ML model performance at the example of chemical toxicity data. Sci Rep 2022; 12:7244. [PMID: 35508546 PMCID: PMC9068909 DOI: 10.1038/s41598-022-09309-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
Machine learning models are widely applied to predict molecular properties or the biological activity of small molecules on a specific protein. Models can be integrated in a conformal prediction (CP) framework which adds a calibration step to estimate the confidence of the predictions. CP models present the advantage of ensuring a predefined error rate under the assumption that test and calibration set are exchangeable. In cases where the test data have drifted away from the descriptor space of the training data, or where assay setups have changed, this assumption might not be fulfilled and the models are not guaranteed to be valid. In this study, the performance of internally valid CP models when applied to either newer time-split data or to external data was evaluated. In detail, temporal data drifts were analysed based on twelve datasets from the ChEMBL database. In addition, discrepancies between models trained on publicly-available data and applied to proprietary data for the liver toxicity and MNT in vivo endpoints were investigated. In most cases, a drastic decrease in the validity of the models was observed when applied to the time-split or external (holdout) test sets. To overcome the decrease in model validity, a strategy for updating the calibration set with data more similar to the holdout set was investigated. Updating the calibration set generally improved the validity, restoring it completely to its expected value in many cases. The restored validity is the first requisite for applying the CP models with confidence. However, the increased validity comes at the cost of a decrease in model efficiency, as more predictions are identified as inconclusive. This study presents a strategy to recalibrate CP models to mitigate the effects of data drifts. Updating the calibration sets without having to retrain the model has proven to be a useful approach to restore the validity of most models.
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Affiliation(s)
- Andrea Morger
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Marina Garcia de Lomana
- BASF SE, 67056, Ludwigshafen, Germany
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Ulf Norinder
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, 751 24, Sweden
- Dept Computer and Systems Sciences, Stockholm University, Kista, 164 07, Sweden
- MTM Research Centre, School of Science and Technology, 701 82, Örebro, Sweden
| | - Fredrik Svensson
- Alzheimer's Research UK UCL Drug Discovery Institute, London, WC1E 6BT, UK
| | - Johannes Kirchmair
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | | | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
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R Packages for Data Quality Assessments and Data Monitoring: A Software Scoping Review with Recommendations for Future Developments. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Data quality assessments (DQA) are necessary to ensure valid research results. Despite the growing availability of tools of relevance for DQA in the R language, a systematic comparison of their functionalities is missing. Therefore, we review R packages related to data quality (DQ) and assess their scope against a DQ framework for observational health studies. Based on a systematic search, we screened more than 140 R packages related to DQA in the Comprehensive R Archive Network. From these, we selected packages which target at least three of the four DQ dimensions (integrity, completeness, consistency, accuracy) in a reference framework. We evaluated the resulting 27 packages for general features (e.g., usability, metadata handling, output types, descriptive statistics) and the possible assessment’s breadth. To facilitate comparisons, we applied all packages to a publicly available dataset from a cohort study. We found that the packages’ scope varies considerably regarding functionalities and usability. Only three packages follow a DQ concept, and some offer an extensive rule-based issue analysis. However, the reference framework does not include a few implemented functionalities, and it should be broadened accordingly. Improved use of metadata to empower DQA and user-friendliness enhancement, such as GUIs and reports that grade the severity of DQ issues, stand out as the main directions for future developments.
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Alka O, Shanthamoorthy P, Witting M, Kleigrewe K, Kohlbacher O, Röst HL. DIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics. Nat Commun 2022; 13:1347. [PMID: 35292629 PMCID: PMC8924252 DOI: 10.1038/s41467-022-29006-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Abstract
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges of data-independent acquisition results and their filtering. Another factor is that the creation of assay libraries for data-independent acquisition analysis and the processing of extracted ion chromatograms have not been automated in metabolomics. Here we present a fully automated open-source workflow for high-throughput metabolomics that combines data-dependent and data-independent acquisition for library generation, analysis, and statistical validation, with rigorous control of the false-discovery rate while matching manual analysis regarding quantification accuracy. Using an experimentally specific data-dependent acquisition library based on reference substances allows for accurate identification of compounds and markers from data-independent acquisition data in low concentrations, facilitating biomarker quantification.
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Affiliation(s)
- Oliver Alka
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
| | - Premy Shanthamoorthy
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Analytical Food Chemistry, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Oliver Kohlbacher
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Hannes L Röst
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
- Department of Computer Science, University of Toronto, Toronto, Canada.
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Soiland-Reyes S, Bayarri G, Andrio P, Long R, Lowe D, Niewielska A, Hospital A, Groth P. Making Canonical Workflow Building Blocks Interoperable across Workflow Languages. DATA INTELLIGENCE 2022. [DOI: 10.1162/dint_a_00135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Abstract
We introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms. The concept is implemented and demonstrated with the BioExcel Building Blocks library (BioBB), a collection of tool wrappers in the field of computational biomolecular simulation. Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow, built using this library and run with 5 different Workflow Manager Systems (WfMS). We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research (CWFR) in order to improve widespread adoption and reuse of computational methods across workflow language barriers.
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Affiliation(s)
- Stian Soiland-Reyes
- Department of Computer Science, The University of Manchester, Manchester, Manchester M13 9PL, UK
- Informatics Institute, University of Amsterdam, Amsterdam 1000 GG, The Nehterlands
| | - Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Pau Andrio
- The Spanish National Bioinformatics Institute (INB), Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Robin Long
- Data Science Institute, Lancaster University, Lancaster, Lancashire LA1 4YW, UK
- Research IT, IT Services, The University of Manchester, Manchester, Manchester M13 9PL, UK
| | - Douglas Lowe
- Research IT, IT Services, The University of Manchester, Manchester, Manchester M13 9PL, UK
| | - Ania Niewielska
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Paul Groth
- Informatics Institute, University of Amsterdam, Amsterdam 1000 GG, The Nehterlands
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Watson ER, Taherian Fard A, Mar JC. Computational Methods for Single-Cell Imaging and Omics Data Integration. Front Mol Biosci 2022; 8:768106. [PMID: 35111809 PMCID: PMC8801747 DOI: 10.3389/fmolb.2021.768106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.
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Affiliation(s)
| | - Atefeh Taherian Fard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Jessica Cara Mar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
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41
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Noor A. Improving bioinformatics software quality through incorporation of software engineering practices. PeerJ Comput Sci 2022; 8:e839. [PMID: 35111923 PMCID: PMC8771759 DOI: 10.7717/peerj-cs.839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Bioinformatics software is developed for collecting, analyzing, integrating, and interpreting life science datasets that are often enormous. Bioinformatics engineers often lack the software engineering skills necessary for developing robust, maintainable, reusable software. This study presents review and discussion of the findings and efforts made to improve the quality of bioinformatics software. METHODOLOGY A systematic review was conducted of related literature that identifies core software engineering concepts for improving bioinformatics software development: requirements gathering, documentation, testing, and integration. The findings are presented with the aim of illuminating trends within the research that could lead to viable solutions to the struggles faced by bioinformatics engineers when developing scientific software. RESULTS The findings suggest that bioinformatics engineers could significantly benefit from the incorporation of software engineering principles into their development efforts. This leads to suggestion of both cultural changes within bioinformatics research communities as well as adoption of software engineering disciplines into the formal education of bioinformatics engineers. Open management of scientific bioinformatics development projects can result in improved software quality through collaboration amongst both bioinformatics engineers and software engineers. CONCLUSIONS While strides have been made both in identification and solution of issues of particular import to bioinformatics software development, there is still room for improvement in terms of shifts in both the formal education of bioinformatics engineers as well as the culture and approaches of managing scientific bioinformatics research and development efforts.
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Jukič M, Kores K, Janežič D, Bren U. Repurposing of Drugs for SARS-CoV-2 Using Inverse Docking Fingerprints. Front Chem 2021; 9:757826. [PMID: 35028304 PMCID: PMC8748264 DOI: 10.3389/fchem.2021.757826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 is a virus that belongs to the Coronaviridae family. This group of viruses commonly causes colds but possesses a tremendous pathogenic potential. In humans, an outbreak of SARS caused by the SARS-CoV virus was first reported in 2003, followed by 2012 when the Middle East respiratory syndrome coronavirus (MERS-CoV) led to an outbreak of Middle East respiratory syndrome (MERS). Moreover, COVID-19 represents a serious socioeconomic and global health problem that has already claimed more than four million lives. To date, there are only a handful of therapeutic options to combat this disease, and only a single direct-acting antiviral, the conditionally approved remdesivir. Since there is an urgent need for active drugs against SARS-CoV-2, the strategy of drug repurposing represents one of the fastest ways to achieve this goal. An in silico drug repurposing study using two methods was conducted. A structure-based virtual screening of the FDA-approved drug database on SARS-CoV-2 main protease was performed, and the 11 highest-scoring compounds with known 3CLpro activity were identified while the methodology was used to report further 11 potential and completely novel 3CLpro inhibitors. Then, inverse molecular docking was performed on the entire viral protein database as well as on the Coronaviridae family protein subset to examine the hit compounds in detail. Instead of target fishing, inverse docking fingerprints were generated for each hit compound as well as for the five most frequently reported and direct-acting repurposed drugs that served as controls. In this way, the target-hitting space was examined and compared and we can support the further biological evaluation of all 11 newly reported hits on SARS-CoV-2 3CLpro as well as recommend further in-depth studies on antihelminthic class member compounds. The authors acknowledge the general usefulness of this approach for a full-fledged inverse docking fingerprint screening in the future.
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Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Katarina Kores
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
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Samuel ELG, Holmes SL, Young DW. Processing binding data using an open-source workflow. J Cheminform 2021; 13:99. [PMID: 34895330 PMCID: PMC8666039 DOI: 10.1186/s13321-021-00577-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There are several approaches that aim to streamline this process, but most involve proprietary software, programming knowledge, or are designed for specific instrument output files. We therefore developed an analysis workflow implemented in the Konstanz Information Miner (KNIME), a free and open-source data analytics platform, which greatly streamlined our data processing timeline for 384-well plates. The implementation is code-free and freely available to the community for improvement and customization to accommodate a wide range of instrument input files and workflows. ![]()
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Affiliation(s)
- Errol L G Samuel
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Secondra L Holmes
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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44
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Phanchana M, Harnvoravongchai P, Wongkuna S, Phetruen T, Phothichaisri W, Panturat S, Pipatthana M, Charoensutthivarakul S, Chankhamhaengdecha S, Janvilisri T. Frontiers in antibiotic alternatives for Clostridioides difficile infection. World J Gastroenterol 2021; 27:7210-7232. [PMID: 34876784 PMCID: PMC8611198 DOI: 10.3748/wjg.v27.i42.7210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/12/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile (C. difficile) is a gram-positive, anaerobic spore-forming bacterium and a major cause of antibiotic-associated diarrhea. Humans are naturally resistant to C. difficile infection (CDI) owing to the protection provided by healthy gut microbiota. When the gut microbiota is disturbed, C. difficile can colonize, produce toxins, and manifest clinical symptoms, ranging from asymptomatic diarrhea and colitis to death. Despite the steady-if not rising-prevalence of CDI, it will certainly become more problematic in a world of antibiotic overuse and the post-antibiotic era. C. difficile is naturally resistant to most of the currently used antibiotics as it uses multiple resistance mechanisms. Therefore, current CDI treatment regimens are extremely limited to only a few antibiotics, which include vancomycin, fidaxomicin, and metronidazole. Therefore, one of the main challenges experienced by the scientific community is the development of alternative approaches to control and treat CDI. In this Frontier article, we collectively summarize recent advances in alternative treatment approaches for CDI. Over the past few years, several studies have reported on natural product-derived compounds, drug repurposing, high-throughput library screening, phage therapy, and fecal microbiota transplantation. We also include an update on vaccine development, pre- and pro-biotics for CDI, and toxin antidote approaches. These measures tackle CDI at every stage of disease pathology via multiple mechanisms. We also discuss the gaps and concerns in these developments. The next epidemic of CDI is not a matter of if but a matter of when. Therefore, being well-equipped with a collection of alternative therapeutics is necessary and should be prioritized.
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Affiliation(s)
- Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | | | - Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Supakan Panturat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Methinee Pipatthana
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sitthivut Charoensutthivarakul
- School of Bioinnovation and Bio-based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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45
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Yang ZY, Fu L, Lu AP, Liu S, Hou TJ, Cao DS. Semi-automated workflow for molecular pair analysis and QSAR-assisted transformation space expansion. J Cheminform 2021; 13:86. [PMID: 34774096 PMCID: PMC8590336 DOI: 10.1186/s13321-021-00564-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/30/2021] [Indexed: 12/01/2022] Open
Abstract
In the process of drug discovery, the optimization of lead compounds has always been a challenge faced by pharmaceutical chemists. Matched molecular pair analysis (MMPA), a promising tool to efficiently extract and summarize the relationship between structural transformation and property change, is suitable for local structural optimization tasks. Especially, the integration of MMPA with QSAR modeling can further strengthen the utility of MMPA in molecular optimization navigation. In this study, a new semi-automated procedure based on KNIME was developed to support MMPA on both large- and small-scale datasets, including molecular preparation, QSAR model construction, applicability domain evaluation, and MMP calculation and application. Two examples covering regression and classification tasks were provided to gain a better understanding of the importance of MMPA, which has also shown the reliability and utility of this MMPA-by-QSAR pipeline. ![]()
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Affiliation(s)
- Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China.,Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, 410013, Hunan, China
| | - Li Fu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China.,Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, 410013, Hunan, China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, 999077, SAR, People's Republic of China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China. .,Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, 410013, Hunan, China. .,Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, 999077, SAR, People's Republic of China.
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Kolar K, Dondorp D, Zwiggelaar JC, Høyer J, Chatzigeorgiou M. Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data. Nat Commun 2021; 12:6569. [PMID: 34772921 PMCID: PMC8589933 DOI: 10.1038/s41467-021-26550-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 10/13/2021] [Indexed: 01/09/2023] Open
Abstract
Calcium imaging is an increasingly valuable technique for understanding neural circuits, neuroethology, and cellular mechanisms. The analysis of calcium imaging data presents challenges in image processing, data organization, analysis, and accessibility. Tools have been created to address these problems independently, however a comprehensive user-friendly package does not exist. Here we present Mesmerize, an efficient, expandable and user-friendly analysis platform, which uses a Findable, Accessible, Interoperable and Reproducible (FAIR) system to encapsulate the entire analysis process, from raw data to interactive visualizations for publication. Mesmerize provides a user-friendly graphical interface to state-of-the-art analysis methods for signal extraction & downstream analysis. We demonstrate the broad scientific scope of Mesmerize's applications by analyzing neuronal datasets from mouse and a volumetric zebrafish dataset. We also applied contemporary time-series analysis techniques to analyze a novel dataset comprising neuronal, epidermal, and migratory mesenchymal cells of the protochordate Ciona intestinalis.
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Affiliation(s)
- Kushal Kolar
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway.
| | - Daniel Dondorp
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway
| | | | - Jørgen Høyer
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway
| | - Marios Chatzigeorgiou
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway.
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47
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Wang M, Hou S, Liu Y, Li D, Lin J. Identification of Novel Antagonists Targeting Cannabinoid Receptor 2 Using a Multi-Step Virtual Screening Strategy. Molecules 2021; 26:molecules26216679. [PMID: 34771087 PMCID: PMC8587544 DOI: 10.3390/molecules26216679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022] Open
Abstract
The endocannabinoid system plays an essential role in the regulation of analgesia and human immunity, and Cannabinoid Receptor 2 (CB2) has been proved to be an ideal target for the treatment of liver diseases and some cancers. In this study, we identified CB2 antagonists using a three-step “deep learning–pharmacophore–molecular docking” virtual screening approach. From the ChemDiv database (1,178,506 compounds), 15 hits were selected and tested by radioligand binding assays and cAMP functional assays. A total of 7 out of the 15 hits were found to exhibit binding affinities in the radioligand binding assays against CB2 receptor, with a pKi of 5.15–6.66, among which five compounds showed antagonistic activities with pIC50 of 5.25–6.93 in the cAMP functional assays. Among these hits, Compound 8 with the 4H-pyrido[1,2-a]pyrimidin-4-one scaffold showed the best binding affinity and antagonistic activity with a pKi of 6.66 and pIC50 of 6.93, respectively. The new scaffold could serve as a lead for further development of CB2 drugs. Additionally, we hope that the model in this study could be further utilized to identify more novel CB2 receptor antagonists, and the developed approach could also be used to design potent ligands for other therapeutic targets.
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Affiliation(s)
- Mukuo Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (M.W.); (S.H.); (Y.L.)
| | - Shujing Hou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (M.W.); (S.H.); (Y.L.)
| | - Ye Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (M.W.); (S.H.); (Y.L.)
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (M.W.); (S.H.); (Y.L.)
- Correspondence: (D.L.); (J.L.)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (M.W.); (S.H.); (Y.L.)
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300457, China
- Correspondence: (D.L.); (J.L.)
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48
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Balluet M, Sizaire F, El Habouz Y, Walter T, Pont J, Giroux B, Bouchareb O, Tramier M, Pecreaux J. Neural network fast-classifies biological images through features selecting to power automated microscopy. J Microsc 2021; 285:3-19. [PMID: 34623634 DOI: 10.1111/jmi.13062] [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: 03/15/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
Abstract
Artificial intelligence is nowadays used for cell detection and classification in optical microscopy during post-acquisition analysis. The microscopes are now fully automated and next expected to be smart by making acquisition decisions based on the images. It calls for analysing them on the fly. Biology further imposes training on a reduced data set due to cost and time to prepare the samples and have the data sets annotated by experts. We propose a real-time image processing compliant with these specifications by balancing accurate detection and execution performance. We characterised the images using a generic, high-dimensional feature extractor. We then classified the images using machine learning to understand the contribution of each feature in decision and execution time. We found that the non-linear-classifier random forests outperformed Fisher's linear discriminant. More importantly, the most discriminant and time-consuming features could be excluded without significant accuracy loss, offering a substantial gain in execution time. It suggests a feature-group redundancy likely related to the biology of the observed cells. We offer a method to select fast and discriminant features. In our assay, a 79.6 ± 2.4% accurate classification of a cell took 68.7 ± 3.5 ms (mean ± SD, 5-fold cross-validation nested in 10 bootstrap repeats), corresponding to 14 cells per second, dispatched into eight phases of the cell cycle, using 12 feature groups and operating a consumer market ARM-based embedded system. A simple neural network offered similar performances paving the way to faster training and classification, using parallel execution on a general-purpose graphic processing unit. Finally, this strategy is also usable for deep neural networks paving the way to optimizing these algorithms for smart microscopy.
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Affiliation(s)
- Maël Balluet
- CNRS, Univ Rennes, IGDR - UMR 6290, Rennes, France.,Inscoper SAS, Cesson-Sévigné, France
| | - Florian Sizaire
- CNRS, Univ Rennes, IGDR - UMR 6290, Rennes, France.,Present address Biologics Research, Sanofi R&D, Vitry-sur-Seine, France
| | | | - Thomas Walter
- Centre for Computational Biology (CBIO), MINES ParisTech, PSL University, Paris, France.,Institut Curie, Paris, France.,INSERM, U900, Paris, France
| | | | | | | | - Marc Tramier
- CNRS, Univ Rennes, IGDR - UMR 6290, Rennes, France.,Univ Rennes, BIOSIT, UMS CNRS 3480, US INSERM 018, Rennes, France
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Wratten L, Wilm A, Göke J. Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nat Methods 2021; 18:1161-1168. [PMID: 34556866 DOI: 10.1038/s41592-021-01254-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
Abstract
The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not just for experiments, but also for computational analysis. However, transforming data into information involves running a large number of tools, optimizing parameters, and integrating dynamically changing reference data. Workflow managers were developed in response to such challenges. They simplify pipeline development, optimize resource usage, handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing. In this Perspective, we highlight key features of workflow managers, compare commonly used approaches for bioinformatics workflows, and provide a guide for computational and noncomputational users. We outline community-curated pipeline initiatives that enable novice and experienced users to perform complex, best-practice analyses without having to manually assemble workflows. In sum, we illustrate how workflow managers contribute to making computational analysis in biomedical research shareable, scalable, and reproducible.
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Affiliation(s)
| | | | - Jonathan Göke
- Genome Institute of Singapore, Singapore, Singapore.
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50
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Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Curr Protoc 2021; 1:e89. [PMID: 34038030 DOI: 10.1002/cpz1.89] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. ImageJ's traditional strength is in single-image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. Although many image analysis problems can be well solved with one or the other, using these two platforms together in a single workflow can be powerful. Here, we share two pipelines demonstrating mechanisms for productively and conveniently integrating ImageJ and CellProfiler for (1) studying cell morphology and migration via tracking, and (2) advanced stitching techniques for handling large, tiled image sets to improve segmentation. No single platform can provide all the key and most efficient functionality needed for all studies. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. ImageJ and CellProfiler are both committed to interoperability between their platforms, with ongoing development to improve how both are leveraged from the other. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Studying cell morphology and cell migration in time-lapse datasets using TrackMate (Fiji) and CellProfiler Basic Protocol 2: Creating whole plate montages to easily assess adaptability of segmentation parameters.
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Affiliation(s)
- Ellen T A Dobson
- Laboratory for Optical and Computational Instrumentation (LOCI), Center for Quantitative Cell Imaging, University of Wisconsin at Madison, Madison, Wisconsin
| | - Beth Cimini
- Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Anna H Klemm
- Science for Life Laboratory BioImage Informatics Facility and Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Carolina Wählby
- Science for Life Laboratory BioImage Informatics Facility and Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation (LOCI), Center for Quantitative Cell Imaging, University of Wisconsin at Madison, Madison, Wisconsin.,Department of Medical Physics, University of Wisconsin at Madison, Madison, Wisconsin.,Morgridge Institute for Research, Madison, Wisconsin
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