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Blanke G, Brammer J, Baljozovic D, Khan NU, Lange F, Bänsch F, Tovee CA, Schatzschneider U, Hartshorn RM, Herres-Pawlis S. Making the InChI FAIR and sustainable while moving to inorganics. Faraday Discuss 2024. [PMID: 39355958 DOI: 10.1039/d4fd00145a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
The InChI (International Chemical Identifier) standard stands as a cornerstone in chemical informatics, facilitating the structure-based identification and exchange chemical information about compounds across various platforms and databases. The InChI as a unique canonical line notation has made chemical structures searchable on the internet at a broad scale. The largest repositories working with InChIs contain more than 1 billion structures. Central to the functionality of the InChI is its codebase, which orchestrates a series of intricate steps to generate unique identifiers for chemical compounds. Up to now, these steps have been sparsely documented and the InChI algorithm had to be seen as a black box. For the new v1.07 release, the code has been analyzed and the major steps documented, more than 3000 bugs and security issues, as well as nearly 60 Google OSS-Fuzz issues have been fixed. New test systems have been implemented that allow users to directly test the code developments. The move to GitHub has not only made the development more transparent but will also enable external contributors to join the further development of the InChI code. Motivation for this modernisation was the urgency to treat molecular inorganic compounds by the InChI in a meaningful way. Until now, no classic string representation fulfills this need of molecular inorganic chemistry. Currently bonds to metal centers are by definition disconnected which makes most inorganic InChIs meaningless at the moment. Herein, we propose new routines to remedy this problem in the representation of molecular inorganic compounds by the InChI.
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Affiliation(s)
| | - Jan Brammer
- Institut für Anorganische Chemie, Landoltweg 1a, 52074 Aachen, Germany.
| | | | - Nauman Ullah Khan
- Institut für Anorganische Chemie, Landoltweg 1a, 52074 Aachen, Germany.
| | - Frank Lange
- Institut für Anorganische Chemie, Landoltweg 1a, 52074 Aachen, Germany.
| | - Felix Bänsch
- Beilstein-Institut zur Förderung der Chemischen Wissenschaften, Trakehner Straße 7-9, 60487 Frankfurt am Main, Germany
| | - Clare A Tovee
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK
| | - Ulrich Schatzschneider
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Richard M Hartshorn
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
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Ryzhkov FV, Ryzhkova YE, Elinson MN. Python tools for structural tasks in chemistry. Mol Divers 2024:10.1007/s11030-024-10889-7. [PMID: 38744790 DOI: 10.1007/s11030-024-10889-7] [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: 03/14/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024]
Abstract
In recent decades, the use of computational approaches and artificial intelligence in the scientific environment has become more widespread. In this regard, the popular and versatile programming language Python has attracted considerable attention from scientists in the field of chemistry. It is used to solve a variety of chemical and structural problems, including calculating descriptors, molecular fingerprints, graph construction, and computing chemical reaction networks. Python offers high-quality visualization tools for analyzing chemical spaces and compound libraries. This review is a list of tools for the above tasks, including scripts, libraries, ready-made programs, and web interfaces. Inevitably this manuscript does not claim to be an all-encompassing handbook including all the existing Python-based structural chemistry codes. The review serves as a starting point for scientists wishing to apply automatization or optimization to routine chemistry problems.
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Affiliation(s)
- Fedor V Ryzhkov
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky Prospekt, Moscow, 119991, Russia.
| | - Yuliya E Ryzhkova
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky Prospekt, Moscow, 119991, Russia
| | - Michail N Elinson
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky Prospekt, Moscow, 119991, Russia
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3
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Qian W, Lu J, Gao C, Liu Q, Li Y, Zeng Q, Zhang J, Wang T, Chen S. Deciphering antifungal and antibiofilm mechanisms of isobavachalcone against Cryptococcus neoformans through RNA-seq and functional analyses. Microb Cell Fact 2024; 23:107. [PMID: 38609931 PMCID: PMC11015616 DOI: 10.1186/s12934-024-02369-2] [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: 01/08/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Cryptococcus neoformans has been designated as critical fungal pathogens by the World Health Organization, mainly due to limited treatment options and the prevalence of antifungal resistance. Consequently, the utilization of novel antifungal agents is crucial for the effective treatment of C. neoformans infections. This study exposed that the minimum inhibitory concentration (MIC) of isobavachalcone (IBC) against C. neoformans H99 was 8 µg/mL, and IBC dispersed 48-h mature biofilms by affecting cell viability at 16 µg/mL. The antifungal efficacy of IBC was further validated through microscopic observations using specific dyes and in vitro assays, which confirmed the disruption of cell wall/membrane integrity. RNA-Seq analysis was employed to decipher the effect of IBC on the C. neoformans H99 transcriptomic profiles. Real-time quantitative reverse transcription PCR (RT-qPCR) analysis was performed to validate the transcriptomic data and identify the differentially expressed genes. The results showed that IBC exhibited various mechanisms to impede the growth, biofilm formation, and virulence of C. neoformans H99 by modulating multiple dysregulated pathways related to cell wall/membrane, drug resistance, apoptosis, and mitochondrial homeostasis. The transcriptomic findings were corroborated by the antioxidant analyses, antifungal drug sensitivity, molecular docking, capsule, and melanin assays. In vivo antifungal activity analysis demonstrated that IBC extended the lifespan of C. neoformans-infected Caenorhabditis elegans. Overall, the current study unveiled that IBC targeted multiple pathways simultaneously to inhibit growth significantly, biofilm formation, and virulence, as well as to disperse mature biofilms of C. neoformans H99 and induce cell death.
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Affiliation(s)
- Weidong Qian
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China.
| | - Jiaxing Lu
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Chang Gao
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Qiming Liu
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Yongdong Li
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, P. R. China
| | - Qiao Zeng
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Jian Zhang
- School of Pharmaceutical Sciences, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Ting Wang
- School of Biological and Pharmaceutical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Si Chen
- Department of Immunology, Shenzhen University Medical School, Shenzhen, 518060, China.
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4
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Orsi M, Shing Loh B, Weng C, Ang WH, Frei A. Using Machine Learning to Predict the Antibacterial Activity of Ruthenium Complexes. Angew Chem Int Ed Engl 2024; 63:e202317901. [PMID: 38088924 DOI: 10.1002/anie.202317901] [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: 11/23/2023] [Indexed: 01/26/2024]
Abstract
Rising antimicrobial resistance (AMR) and lack of innovation in the antibiotic pipeline necessitate novel approaches to discovering new drugs. Metal complexes have proven to be promising antimicrobial compounds, but the number of studied compounds is still low compared to the millions of organic molecules investigated so far. Lately, machine learning (ML) has emerged as a valuable tool for guiding the design of small organic molecules, potentially even in low-data scenarios. For the first time, we extend the application of ML to the discovery of metal-based medicines. Utilising 288 modularly synthesized ruthenium arene Schiff-base complexes and their antibacterial properties, a series of ML models were trained. The models perform well and are used to predict the activity of 54 new compounds. These displayed a 5.7x higher hit-rate (53.7 %) against methicillin-resistant Staphylococcus aureus (MRSA) compared to the original library (9.4 %), demonstrating that ML can be applied to improve the success-rates in the search of new metalloantibiotics. This work paves the way for more ambitious applications of ML in the field of metal-based drug discovery.
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Affiliation(s)
- Markus Orsi
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Boon Shing Loh
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Cheng Weng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
- NUS Graduate School - Integrated Science and Engineering Programme (ISEP), National University of Singapore, 21 Lower Kent Ridge Rd, Singapore, 119077, Singapore
| | - Angelo Frei
- Department of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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Frei A, Verderosa AD, Elliott AG, Zuegg J, Blaskovich MAT. Metals to combat antimicrobial resistance. Nat Rev Chem 2023; 7:202-224. [PMID: 37117903 PMCID: PMC9907218 DOI: 10.1038/s41570-023-00463-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 109.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2023] [Indexed: 02/10/2023]
Abstract
Bacteria, similar to most organisms, have a love-hate relationship with metals: a specific metal may be essential for survival yet toxic in certain forms and concentrations. Metal ions have a long history of antimicrobial activity and have received increasing attention in recent years owing to the rise of antimicrobial resistance. The search for antibacterial agents now encompasses metal ions, nanoparticles and metal complexes with antimicrobial activity ('metalloantibiotics'). Although yet to be advanced to the clinic, metalloantibiotics are a vast and underexplored group of compounds that could lead to a much-needed new class of antibiotics. This Review summarizes recent developments in this growing field, focusing on advances in the development of metalloantibiotics, in particular, those for which the mechanism of action has been investigated. We also provide an overview of alternative uses of metal complexes to combat bacterial infections, including antimicrobial photodynamic therapy and radionuclide diagnosis of bacterial infections.
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Affiliation(s)
- Angelo Frei
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Anthony D Verderosa
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alysha G Elliott
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Johannes Zuegg
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Mark A T Blaskovich
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
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The current landscape of author guidelines in chemistry through the lens of research data sharing. PURE APPL CHEM 2023. [DOI: 10.1515/pac-2022-1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Abstract
As the primary method of communicating research results, journals garner an enormous impact on community behavior. Publishing the underlying research data alongside journal articles is widely considered good scientific practice. Ideally, journals and their publishers place these recommendations or requirements in their author guidelines and data policies. Several efforts are working to improve the infrastructure, processes, and uptake of research data sharing, including the NFDI4Chem consortium, working groups within the RDA, and IUPAC, including the WorldFAIR Chemistry project. In this article, we present the results of a large-scale analysis of author guidelines from several publishers and journals active in chemistry research, showing how well the publishing
landscape supports different criteria and where there is room for improvement. While the requirement for deposition of X-ray diffraction data is commonplace, guidelines rarely mention machine-readable chemical structures and metadata/minimum information standards. Further evaluation criteria included recommendations on persistent identifiers, data availability statements, data deposition into repositories as well as of open analytical data formats. Our survey shows that publishers and journals are starting to include aspects of research data in their guidelines. We as authors should accept and embrace the guidelines with increasing requirements for data availability, data interoperability, and re-usability to improve chemistry research.
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Reiser P, Neubert M, Eberhard A, Torresi L, Zhou C, Shao C, Metni H, van Hoesel C, Schopmans H, Sommer T, Friederich P. Graph neural networks for materials science and chemistry. COMMUNICATIONS MATERIALS 2022; 3:93. [PMID: 36468086 PMCID: PMC9702700 DOI: 10.1038/s43246-022-00315-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/07/2022] [Indexed: 05/14/2023]
Abstract
Machine learning plays an increasingly important role in many areas of chemistry and materials science, being used to predict materials properties, accelerate simulations, design new structures, and predict synthesis routes of new materials. Graph neural networks (GNNs) are one of the fastest growing classes of machine learning models. They are of particular relevance for chemistry and materials science, as they directly work on a graph or structural representation of molecules and materials and therefore have full access to all relevant information required to characterize materials. In this Review, we provide an overview of the basic principles of GNNs, widely used datasets, and state-of-the-art architectures, followed by a discussion of a wide range of recent applications of GNNs in chemistry and materials science, and concluding with a road-map for the further development and application of GNNs.
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Affiliation(s)
- Patrick Reiser
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Marlen Neubert
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - André Eberhard
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - Luca Torresi
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - Chen Zhou
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - Chen Shao
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Present Address: Institute for Applied Informatics and Formal Description Systems, Karlsruhe Institute of Technology, Kaiserstr. 89, 76133 Karlsruhe, Germany
| | - Houssam Metni
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- ECPM, Université de Strasbourg, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Clint van Hoesel
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Department of Applied Physics, Eindhoven University of Technology, Groene Loper 19, 5612 AP Eindhoven, The Netherlands
| | - Henrik Schopmans
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Timo Sommer
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute for Theory of Condensed Matter, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Present Address: School of Chemistry, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Pascal Friederich
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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