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Kwon JH, Kim J, Lim KM, Kim MG. Integration of the Natural Language Processing of Structural Information Simplified Molecular-Input Line-Entry System Can Improve the In Vitro Prediction of Human Skin Sensitizers. TOXICS 2024; 12:153. [PMID: 38393248 PMCID: PMC10892072 DOI: 10.3390/toxics12020153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/03/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
Natural language processing (NLP) technology has recently used to predict substance properties based on their Simplified Molecular-Input Line-Entry System (SMILES). We aimed to develop a model predicting human skin sensitizers by integrating text features derived from SMILES with in vitro test outcomes. The dataset on SMILES, physicochemical properties, in vitro tests (DPRA, KeratinoSensTM, h-CLAT, and SENS-IS assays), and human potency categories for 122 substances sourced from the Cosmetics Europe database. The ChemBERTa model was employed to analyze the SMILES of substances. The last hidden layer embedding of ChemBERTa was tested with other features. Given the modest dataset size, we trained five XGBoost models using subsets of the training data, and subsequently employed bagging to create the final model. Notably, the features computed from SMILES played a pivotal role in the model for distinguishing sensitizers and non-sensitizers. The final model demonstrated a classification accuracy of 80% and an AUC-ROC of 0.82, effectively discriminating sensitizers from non-sensitizers. Furthermore, the model exhibited an accuracy of 82% and an AUC-ROC of 0.82 in classifying strong and weak sensitizers. In summary, we demonstrated that the integration of NLP of SMILES with in vitro test results can enhance the prediction of health hazard associated with chemicals.
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Affiliation(s)
| | | | - Kyung-Min Lim
- College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea; (J.-H.K.); (J.K.)
| | - Myeong Gyu Kim
- College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea; (J.-H.K.); (J.K.)
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Tran TTV, Surya Wibowo A, Tayara H, Chong KT. Artificial Intelligence in Drug Toxicity Prediction: Recent Advances, Challenges, and Future Perspectives. J Chem Inf Model 2023; 63:2628-2643. [PMID: 37125780 DOI: 10.1021/acs.jcim.3c00200] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Toxicity prediction is a critical step in the drug discovery process that helps identify and prioritize compounds with the greatest potential for safe and effective use in humans, while also reducing the risk of costly late-stage failures. It is estimated that over 30% of drug candidates are discarded owing to toxicity. Recently, artificial intelligence (AI) has been used to improve drug toxicity prediction as it provides more accurate and efficient methods for identifying the potentially toxic effects of new compounds before they are tested in human clinical trials, thus saving time and money. In this review, we present an overview of recent advances in AI-based drug toxicity prediction, including the use of various machine learning algorithms and deep learning architectures, of six major toxicity properties and Tox21 assay end points. Additionally, we provide a list of public data sources and useful toxicity prediction tools for the research community and highlight the challenges that must be addressed to enhance model performance. Finally, we discuss future perspectives for AI-based drug toxicity prediction. This review can aid researchers in understanding toxicity prediction and pave the way for new methods of drug discovery.
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Affiliation(s)
- Thi Tuyet Van Tran
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Faculty of Information Technology, An Giang University, Long Xuyen 880000, Vietnam
- Vietnam National University - Ho Chi Minh City, Ho Chi Minh 700000, Vietnam
| | - Agung Surya Wibowo
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Electrical Engineering, Telkom University, Bandung 40257, Indonesia
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Kil To Chong
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Pantaleão SQ, Fernandes PO, Gonçalves JE, Maltarollo VG, Honorio KM. Recent Advances in the Prediction of Pharmacokinetics Properties in Drug Design Studies: A Review. ChemMedChem 2021; 17:e202100542. [PMID: 34655454 DOI: 10.1002/cmdc.202100542] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/07/2021] [Indexed: 12/11/2022]
Abstract
This review presents the main aspects related to pharmacokinetic properties, which are essential for the efficacy and safety of drugs. This topic is very important because the analysis of pharmacokinetic aspects in the initial design stages of drug candidates can increase the chances of success for the entire process. In this scenario, experimental and in silico techniques have been widely used. Due to the difficulties encountered with the use of some experimental tests to determine pharmacokinetic properties, several in silico tools have been developed and have shown promising results. Therefore, in this review, we address the main free tools/servers that have been used in this area, as well as some cases of application. Finally, we present some studies that employ a multidisciplinary approach with synergy between in silico, in vitro, and in vivo techniques to assess ADME properties of bioactive substances, achieving successful results in drug discovery and design.
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Affiliation(s)
- Simone Q Pantaleão
- Centro de Ciências Naturais e Humanas, Institution Universidade Federal do ABC, 09210-580, Santo André, SP, Brazil
| | - Philipe O Fernandes
- Departamento de Produtos Farmacêuticos, Universidade Federal de Minas Gerais, 31270-901, Pampulha, MG, Brazil
| | - José Eduardo Gonçalves
- Departamento de Produtos Farmacêuticos, Universidade Federal de Minas Gerais, 31270-901, Pampulha, MG, Brazil
| | - Vinícius G Maltarollo
- Departamento de Produtos Farmacêuticos, Universidade Federal de Minas Gerais, 31270-901, Pampulha, MG, Brazil
| | - Kathia Maria Honorio
- Centro de Ciências Naturais e Humanas, Institution Universidade Federal do ABC, 09210-580, Santo André, SP, Brazil.,Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, 03828-000, São Paulo, SP, Brazil
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Ntie-Kang F, Telukunta KK, Fobofou SAT, Chukwudi Osamor V, Egieyeh SA, Valli M, Djoumbou-Feunang Y, Sorokina M, Stork C, Mathai N, Zierep P, Chávez-Hernández AL, Duran-Frigola M, Babiaka SB, Tematio Fouedjou R, Eni DB, Akame S, Arreyetta-Bawak AB, Ebob OT, Metuge JA, Bekono BD, Isa MA, Onuku R, Shadrack DM, Musyoka TM, Patil VM, van der Hooft JJJ, da Silva Bolzani V, Medina-Franco JL, Kirchmair J, Weber T, Tastan Bishop Ö, Medema MH, Wessjohann LA, Ludwig-Müller J. Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J Cheminform 2021; 13:64. [PMID: 34488889 PMCID: PMC8419829 DOI: 10.1186/s13321-021-00546-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 11/12/2022] Open
Abstract
We report the major conclusions of the online open-access workshop "Computational Applications in Secondary Metabolite Discovery (CAiSMD)" that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from five continents (Africa, Asia, Europe, South America, and North America) took part in the workshop. The workshop highlighted the potential applications of computational methodologies in the search for secondary metabolites (SMs) or natural products (NPs) as potential drugs and drug leads. During 3 days, the participants of this online workshop received an overview of modern computer-based approaches for exploring NP discovery in the "omics" age. The invited experts gave keynote lectures, trained participants in hands-on sessions, and held round table discussions. This was followed by oral presentations with much interaction between the speakers and the audience. Selected applicants (early-career scientists) were offered the opportunity to give oral presentations (15 min) and present posters in the form of flash presentations (5 min) upon submission of an abstract. The final program available on the workshop website ( https://caismd.indiayouth.info/ ) comprised of 4 keynote lectures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on sessions (HSs). This meeting report also references internet resources for computational biology in the area of secondary metabolites that are of use outside of the workshop areas and will constitute a long-term valuable source for the community. The workshop concluded with an online survey form to be completed by speakers and participants for the goal of improving any subsequent editions.
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Affiliation(s)
- Fidele Ntie-Kang
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Kiran K. Telukunta
- Tarunavadaanenasaha Muktbharatonnayana Samstha Foundation, Hyderabad, India
| | - Serge A. T. Fobofou
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, 38106 Braunschweig, Germany
| | - Victor Chukwudi Osamor
- Department of Computer and Information Sciences, Colege of Science and Technology, Covenant University, Km. 10 Idiroko Rd, Ogun Ota, Nigeria
| | - Samuel A. Egieyeh
- School of Pharmacy, University of the Western Cape, Cape Town, 7535 South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, 7535 South Africa
| | - Marilia Valli
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University–UNESP, Araraquara, Brazil
| | | | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Conrad Stork
- Center for Bioinformatics, Universität Hamburg, 20146 Hamburg, Germany
| | - Neann Mathai
- Department of Chemistry and Computational Biology Unit (CBU), University of Bergen, 5020 Bergen, Norway
| | - Paul Zierep
- Pharmaceutical Bioinformatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Ana L. Chávez-Hernández
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miquel Duran-Frigola
- Ersilia Open Source Initiative, Cambridge, UK
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia Spain
| | - Smith B. Babiaka
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | | | - Donatus B. Eni
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Simeon Akame
- Department of Immunology, School of Health Sciences, Catholic University of Central Africa, BP 7871, Yaoundé, Cameroon
| | | | - Oyere T. Ebob
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Jonathan A. Metuge
- Department of Biochemistry and Molecular Biology, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Boris D. Bekono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, BP. 47, Yaoundé, Cameroon
| | - Mustafa A. Isa
- Bioinformatics and Computational Biology Lab, Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State Nigeria
| | - Raphael Onuku
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria Nsukka, Nsukka, Nigeria
| | - Daniel M. Shadrack
- Department of Chemistry, St. John’s University of Tanzania, P. O. Box 47, Dodoma, Tanzania
| | - Thommas M. Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140 South Africa
| | - Vaishali M. Patil
- Computer Aided Drug Design Lab, KIET Group of Institutions, Delhi-NCR, Ghaziabad, 201206 India
| | | | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University–UNESP, Araraquara, Brazil
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140 South Africa
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103 Leipzig, Germany
| | - Jutta Ludwig-Müller
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
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Wilm A, Garcia de Lomana M, Stork C, Mathai N, Hirte S, Norinder U, Kühnl J, Kirchmair J. Predicting the Skin Sensitization Potential of Small Molecules with Machine Learning Models Trained on Biologically Meaningful Descriptors. Pharmaceuticals (Basel) 2021; 14:ph14080790. [PMID: 34451887 PMCID: PMC8402010 DOI: 10.3390/ph14080790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023] Open
Abstract
In recent years, a number of machine learning models for the prediction of the skin sensitization potential of small organic molecules have been reported and become available. These models generally perform well within their applicability domains but, as a result of the use of molecular fingerprints and other non-intuitive descriptors, the interpretability of the existing models is limited. The aim of this work is to develop a strategy to replace the non-intuitive features by predicted outcomes of bioassays. We show that such replacement is indeed possible and that as few as ten interpretable, predicted bioactivities are sufficient to reach competitive performance. On a holdout data set of 257 compounds, the best model (“Skin Doctor CP:Bio”) obtained an efficiency of 0.82 and an MCC of 0.52 (at the significance level of 0.20). Skin Doctor CP:Bio is available free of charge for academic research. The modeling strategies explored in this work are easily transferable and could be adopted for the development of more interpretable machine learning models for the prediction of the bioactivity and toxicity of small organic compounds.
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Affiliation(s)
- Anke Wilm
- Center for Bioinformatics (ZBH), Department of Informatics, Universität Hamburg, 20146 Hamburg, Germany; (A.W.); (C.S.)
- HITeC e.V., 22527 Hamburg, Germany
| | - Marina Garcia de Lomana
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria; (M.G.d.L.); (S.H.)
| | - Conrad Stork
- Center for Bioinformatics (ZBH), Department of Informatics, Universität Hamburg, 20146 Hamburg, Germany; (A.W.); (C.S.)
| | - Neann Mathai
- Computational Biology Unit (CBU), Department of Chemistry, University of Bergen, N-5020 Bergen, Norway;
| | - Steffen Hirte
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria; (M.G.d.L.); (S.H.)
| | - Ulf Norinder
- MTM Research Centre, School of Science and Technology, Örebro University, SE-70182 Örebro, Sweden;
- Department of Computer and Systems Sciences, Stockholm University, SE-16407 Kista, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, SE-75124 Uppsala, Sweden
| | - Jochen Kühnl
- Front End Innovation, Beiersdorf AG, 22529 Hamburg, Germany;
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Universität Hamburg, 20146 Hamburg, Germany; (A.W.); (C.S.)
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria; (M.G.d.L.); (S.H.)
- Correspondence: ; Tel.: +43-1-4277-55104
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Ta GH, Weng CF, Leong MK. In silico Prediction of Skin Sensitization: Quo vadis? Front Pharmacol 2021; 12:655771. [PMID: 34017255 PMCID: PMC8129647 DOI: 10.3389/fphar.2021.655771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/20/2021] [Indexed: 01/10/2023] Open
Abstract
Skin direct contact with chemical or physical substances is predisposed to allergic contact dermatitis (ACD), producing various allergic reactions, namely rash, blister, or itchy, in the contacted skin area. ACD can be triggered by various extremely complicated adverse outcome pathways (AOPs) remains to be causal for biosafety warrant. As such, commercial products such as ointments or cosmetics can fulfill the topically safe requirements in animal and non-animal models including allergy. Europe, nevertheless, has banned animal tests for the safety evaluations of cosmetic ingredients since 2013, followed by other countries. A variety of non-animal in vitro tests addressing different key events of the AOP, the direct peptide reactivity assay (DPRA), KeratinoSens™, LuSens and human cell line activation test h-CLAT and U-SENS™ have been developed and were adopted in OECD test guideline to identify the skin sensitizers. Other methods, such as the SENS-IS are not yet fully validated and regulatorily accepted. A broad spectrum of in silico models, alternatively, to predict skin sensitization have emerged based on various animal and non-animal data using assorted modeling schemes. In this article, we extensively summarize a number of skin sensitization predictive models that can be used in the biopharmaceutics and cosmeceuticals industries as well as their future perspectives, and the underlined challenges are also discussed.
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Affiliation(s)
- Giang Huong Ta
- Department of Chemistry, National Dong Hwa University, Shoufeng, Taiwan
| | - Ching-Feng Weng
- Department of Basic Medical Science, Institute of Respiratory Disease, Xiamen Medical College, Xiamen, China
| | - Max K. Leong
- Department of Chemistry, National Dong Hwa University, Shoufeng, Taiwan
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