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Reed SM. Augmented and Programmatically Optimized LLM Prompts Reduce Chemical Hallucinations. J Chem Inf Model 2025. [PMID: 40262168 DOI: 10.1021/acs.jcim.4c02322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2025]
Abstract
Utilizing large Language models (LLMs) for handling scientific information comes with risk of the outputs not matching expectations, commonly called hallucinations. To fully utilize LLMs in research requires improving their accuracy, avoiding hallucinations, and extending their scope to research topics outside their direct training. There is also a benefit to getting the most accurate information from an LLM at the time of inference without having to create and train custom new models for each application. Here, augmented generation and machine learning-driven prompt optimization are combined to extract performance improvements over base LLM function on a common chemical research task. Specifically, an LLM was used to predict the topological polar surface area (TPSA) of molecules. By using augmented generation and machine learning-optimized prompts, the error in the prediction was reduced to 11.76 root-mean-squared error (RMSE) from 62.34 RMSE with direct calls to the same LLM.
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Affiliation(s)
- Scott M Reed
- Department of Chemistry, University of Colorado Denver, 1151 Arapahoe St., Denver, Colorado 80217-3364, United States
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2
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Sobańska AW, Banerjee A, Roy K. Organic Sunscreens and Their Products of Degradation in Biotic and Abiotic Conditions-In Silico Studies of Drug-Likeness and Human Placental Transport. Int J Mol Sci 2024; 25:12373. [PMID: 39596438 PMCID: PMC11595199 DOI: 10.3390/ijms252212373] [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: 10/10/2024] [Revised: 11/06/2024] [Accepted: 11/15/2024] [Indexed: 11/28/2024] Open
Abstract
A total of 16 organic sunscreens and over 160 products of their degradation in biotic and abiotic conditions were investigated in the context of their safety during pregnancy. Drug-likeness and the ability of the studied compounds to be absorbed from the gastrointestinal tract and cross the human placenta were predicted in silico using the SwissADME software (for drug-likeness and oral absorption) and multiple linear regression and "ARKA" models (for placenta permeability expressed as fetus-to-mother blood concentration in the state of equilibrium), with the latter outperforming the MLR models. It was established that most of the studied compounds can be absorbed from the gastrointestinal tract. The drug-likeness of the studied compounds (expressed as a binary descriptor, Lipinski) is closely related to their ability to cross the placenta (most likely by a passive diffusion mechanism). The organic sunscreens and their degradation products are likely to cross the placenta, except for very bulky and highly lipophilic 1,3,5-triazine derivatives; an avobenzone degradation product, 1,2-bis(4-tert-butylphenyl)ethane-1,2-dione; diethylamino hydroxybenzoyl hexyl benzoate; and dimerization products of sunscreens from the 4-methoxycinnamate group.
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Affiliation(s)
- Anna W. Sobańska
- Department of Analytical Chemistry, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
| | - Arkaprava Banerjee
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India;
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India;
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Ancuceanu R, Popovici PC, Drăgănescu D, Busnatu Ș, Lascu BE, Dinu M. QSAR Regression Models for Predicting HMG-CoA Reductase Inhibition. Pharmaceuticals (Basel) 2024; 17:1448. [PMID: 39598360 PMCID: PMC11597356 DOI: 10.3390/ph17111448] [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: 10/07/2024] [Revised: 10/27/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND/OBJECTIVES HMG-CoA reductase is an enzyme that regulates the initial stage of cholesterol synthesis, and its inhibitors are widely used in the treatment of cardiovascular diseases. METHODS We have created a set of quantitative structure-activity relationship (QSAR) models for human HMG-CoA reductase inhibitors using nested cross-validation as the primary validation method. To develop the QSAR models, we employed various machine learning regression algorithms, feature selection methods, and fingerprints or descriptor datasets. RESULTS We built and evaluated a total of 300 models, selecting 21 that demonstrated good performance (coefficient of determination, R2 ≥ 0.70 or concordance correlation coefficient, CCC ≥ 0.85). Six of these top-performing models met both performance criteria and were used to construct five ensemble models. We identified the descriptors most important in explaining HMG-CoA inhibition for each of the six best-performing models. We used the top models to search through over 220,000 chemical compounds from a large database (ZINC 15) for potential new inhibitors. Only a small fraction (237 out of approximately 220,000 compounds) had reliable predictions with mean pIC50 values ≥ 8 (IC50 values ≤ 10 nM). Our svm-based ensemble model predicted IC50 values < 10 nM for roughly 0.08% of the screened compounds. We have also illustrated the potential applications of these QSAR models in understanding the cholesterol-lowering activities of herbal extracts, such as those reported for an extract prepared from the Iris × germanica rhizome. CONCLUSIONS Our QSAR models can accurately predict human HMG-CoA reductase inhibitors, having the potential to accelerate the discovery of novel cholesterol-lowering agents and may also be applied to understand the mechanisms underlying the reported cholesterol-lowering activities of herbal extracts.
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Affiliation(s)
- Robert Ancuceanu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (R.A.); (P.C.P.); (B.E.L.); (M.D.)
| | - Patriciu Constantin Popovici
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (R.A.); (P.C.P.); (B.E.L.); (M.D.)
| | - Doina Drăgănescu
- Department of Pharmaceutical Physics, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Ștefan Busnatu
- Department of Cardiology, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
- Emergency Hospital “Bagdasar-Arseni”, 050474 Bucharest, Romania
| | - Beatrice Elena Lascu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (R.A.); (P.C.P.); (B.E.L.); (M.D.)
| | - Mihaela Dinu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (R.A.); (P.C.P.); (B.E.L.); (M.D.)
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Vittoria Togo M, Mastrolorito F, Orfino A, Graps EA, Tondo AR, Altomare CD, Ciriaco F, Trisciuzzi D, Nicolotti O, Amoroso N. Where developmental toxicity meets explainable artificial intelligence: state-of-the-art and perspectives. Expert Opin Drug Metab Toxicol 2024; 20:561-577. [PMID: 38141160 DOI: 10.1080/17425255.2023.2298827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023]
Abstract
INTRODUCTION The application of Artificial Intelligence (AI) to predictive toxicology is rapidly increasing, particularly aiming to develop non-testing methods that effectively address ethical concerns and reduce economic costs. In this context, Developmental Toxicity (Dev Tox) stands as a key human health endpoint, especially significant for safeguarding maternal and child well-being. AREAS COVERED This review outlines the existing methods employed in Dev Tox predictions and underscores the benefits of utilizing New Approach Methodologies (NAMs), specifically focusing on eXplainable Artificial Intelligence (XAI), which proves highly efficient in constructing reliable and transparent models aligned with recommendations from international regulatory bodies. EXPERT OPINION The limited availability of high-quality data and the absence of dependable Dev Tox methodologies render XAI an appealing avenue for systematically developing interpretable and transparent models, which hold immense potential for both scientific evaluations and regulatory decision-making.
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Affiliation(s)
- Maria Vittoria Togo
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Fabrizio Mastrolorito
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Angelica Orfino
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Elisabetta Anna Graps
- ARESS Puglia - Agenzia Regionale strategica per laSalute ed il Sociale, Presidenza della Regione Puglia", Bari, Italy
| | - Anna Rita Tondo
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Cosimo Damiano Altomare
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Fulvio Ciriaco
- Department of Chemistry, Universitá degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Daniela Trisciuzzi
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Orazio Nicolotti
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Nicola Amoroso
- Department of Pharmacy - Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", Bari, Italy
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Guan R, Cai R, Guo B, Wang Y, Zhao C. A Data-Driven Computational Framework for Assessing the Risk of Placental Exposure to Environmental Chemicals. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7770-7781. [PMID: 38665120 DOI: 10.1021/acs.est.4c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
A computational framework based on placental gene networks was proposed in this work to improve the accuracy of the placental exposure risk assessment of environmental compounds. The framework quantitatively characterizes the ability of compounds to cross the placental barrier by systematically considering the interaction and pathway-level information on multiple placental transporters. As a result, probability scores were generated for 307 compounds crossing the placental barrier based on this framework. These scores were then used to categorize the compounds into different levels of transplacental transport range, creating a gradient partition. These probability scores not only facilitated a more intuitive understanding of a compound's ability to cross the placental barrier but also provided valuable information for predicting potential placental disruptors. Compounds with probability scores greater than 90% were considered to have significant transplacental transport potential, whereas those with probability scores less than 80% were classified as unlikely to cross the placental barrier. Furthermore, external validation set results showed that the probability score could accurately predict the compounds known to cross the placental barrier. In conclusion, the computational framework proposed in this study enhances the intuitive understanding of the ability of compounds to cross the placental barrier and opens up new avenues for assessing the placental exposure risk of compounds.
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Affiliation(s)
- Ruining Guan
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Ruitong Cai
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Binbin Guo
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yawei Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China
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Gomatam A, Coutinho E. A chirality-sensitive approach to predict chemical transfer across the human placental barrier. Toxicol Lett 2024; 394:66-75. [PMID: 38423482 DOI: 10.1016/j.toxlet.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
The placenta is a membrane that separates the fetus from the maternal circulation, and in addition to protecting the fetus, plays a key role in fetal growth and development. With increasing drug use in pregnancy, it is imperative that reliable models of estimating placental permeability and safety be established. In vitro methods and animal models such as rodent placenta are limited in application since the species-specific nature of the placenta prevents meaningful extrapolations to humans. In this regard, in silico approaches such as quantitative structure-property relationships (QSPRs) are useful alternatives. However, despite evidence that drug transport across the placenta is stereoselective (i.e., governed by the spatial arrangement of the atoms in a molecule), many QSPR models for placental transfer have been built using 2D descriptors that do not account for chirality and stereochemistry. In this study, we apply a chirality-sensitive and proven QSPR methodology titled "EigenValue ANalySis" (EVANS) to build QSPR models for placental transfer. We deploy EVANS along with robust machine learning algorithms to build (i) regression models on a dataset of environmental chemicals (dataset PD I) followed by (ii) classification models on a set of drug-like compounds (dataset PD II). The best models were found to achieve state-of-the-art performance, with the support vector machine algorithm returning rtrain2=0.85,rtest2=0.75 for PD I, and the logistic regression algorithm giving accuracy 0.88 and F1 score 0.93 for PD II. The best models were interpreted with the Shapley Additive Explanations paradigm, and it was found that autocorrelation descriptors are crucial for modelling placental permeability. In conclusion, we demonstrate the need of a chirality-sensitive approach for modelling placental transfer of chemicals, and present two predictive QSPR models that may reliably be used for prediction of placental transfer.
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Affiliation(s)
- Anish Gomatam
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Mumbai, India.
| | - Evans Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Mumbai, India; St. John Institute of Pharmacy and Research, Palghar (E), Palghar, India
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Vukomanović P, Stefanović M, Stevanović JM, Petrić A, Trenkić M, Andrejević L, Lazarević M, Sokolović D, Veselinović AM. Monte Carlo Optimization Method Based QSAR Modeling of Placental Barrier Permeability. Pharm Res 2024; 41:493-500. [PMID: 38337105 DOI: 10.1007/s11095-024-03675-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
PURPOSE In order to ensure that drug administration is safe during pregnancy, it is crucial to have the possibility to predict the placental permeability of drugs in humans. The experimental method which is most widely used for the said purpose is in vitro human placental perfusion, though the approach is highly expensive and time consuming. Quantitative structure-activity relationship (QSAR) modeling represents a powerful tool for the assessment of the drug placental transfer, and can be successfully employed to be an alternative in in vitro experiments. METHODS The conformation-independent QSAR models covered in the present study were developed through the use of the SMILES notation descriptors and local molecular graph invariants. What is more, the Monte Carlo optimization method, was used in the test sets and the training sets as the model developer with three independent molecular splits. RESULTS A range of different statistical parameters was used to validate the developed QSAR model, including the standard error of estimation, mean absolute error, root-mean-square error (RMSE), correlation coefficient, cross-validated correlation coefficient, Fisher ratio, MAE-based metrics and the correlation ideality index. Once the mentioned statistical methods were employed, an excellent predictive potential and robustness of the developed QSAR model was demonstrated. In addition, the molecular fragments, which are derived from the SMILES notation descriptors accounting for the decrease or increase in the investigated activity, were revealed. CONCLUSION The presented QSAR modeling can be an invaluable tool for the high-throughput screening of the placental permeability of drugs.
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Affiliation(s)
- Predrag Vukomanović
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Milan Stefanović
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Jelena Milošević Stevanović
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Aleksandra Petrić
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Milan Trenkić
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Gynecology and Obstetrics, University Clinical Centre of Niš, Niš, Serbia
| | - Lazar Andrejević
- COVID Hospital, University Clinical Centre of Niš, Kruševac, Serbia
| | - Milan Lazarević
- Faculty of Medicine, University of Niš, Niš, Serbia
- Clinic for Cardiovascular and Transplant Surgery, University Clinical Centre of Niš, Niš, Serbia
| | | | - Aleksandar M Veselinović
- Faculty of Medicine, Department of Chemistry, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia.
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8
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Sobańska AW. In silico assessment of risks associated with pesticides exposure during pregnancy. CHEMOSPHERE 2023; 329:138649. [PMID: 37043889 DOI: 10.1016/j.chemosphere.2023.138649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
Novel Quantitative Structure-Activity Relationship (QSAR) models of compounds' placenta (PL) permeability expressed as their log FM (fetus-to-mother blood concentration) values or binary PL1/0 (crossing/non-crossing) score were generated using a number of statistical tools: Multiple Linear Regression, Boosted Trees, Principal Component Analysis and Artificial Neural Networks, on the basis of molecular descriptors calculated by Mordred software and selected using Partial Least Squares (PLS) analysis. It was established that the most important predictor of both log FM and the binary PL1/0 score is Lipinski - a binary variable reflecting the compounds' ability to satisfy the criteria of drug-likeness according to the Lipinski's "Rule of 5". The quantitative (log FM) and qualitative (PL1/0) models of PL permeability were applied to 345 pesticides from different chemical families (triazines, carbamates, pyrethroids, organochlorine, organophosphorus and miscellaneous compounds). The ability of studied pesticides to cross the placenta was assessed; the basic physico-chemical parameters responsible for good or poor placenta transport of pesticides were identified and the relationships between the pesticides' PL permeability, blood-brain barrier (BBB) transfer and gastro-intestinal (GI) absorption were investigated. It was found (on the basis of logistic regression analysis) that the probability of a compound crossing the placenta (PL1) is inversely correlated with its lipophilicity and molar refractivity and positively correlated with the total count of oxygen and nitrogen atoms.
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Affiliation(s)
- Anna W Sobańska
- Department of Analytical Chemistry Medical University of Lodz, 90-151, Łódź, Muszyńskiego 1, Poland.
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Gély CA, Picard-Hagen N, Chassan M, Garrigues JC, Gayrard V, Lacroix MZ. Contribution of Reliable Chromatographic Data in QSAR for Modelling Bisphenol Transport across the Human Placenta Barrier. Molecules 2023; 28:500. [PMID: 36677565 PMCID: PMC9863378 DOI: 10.3390/molecules28020500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Regulatory measures and public concerns regarding bisphenol A (BPA) have led to its replacement by structural analogues, such as BPAF, BPAP, BPB, BPF, BPP, BPS, and BPZ. However, these alternatives are under surveillance for potential endocrine disruption, particularly during the critical period of fetal development. Despite their structural analogies, these BPs differ greatly in their placental transport efficiency. For predicting the fetal exposure of this important class of emerging contaminants, quantitative structure-activity relationship (QSAR) studies were developed to model and predict the placental clearance indices (CI). The most usual input parameters were molecular descriptors obtained by modelling, but for bisphenols (BPs) with structural similarities or heteroatoms such as sulfur, these descriptors do not contrast greatly. This study evaluated and compared the capacity of QSAR models based either on molecular or chromatographic descriptors or a combination of both to predict the placental passage of BPs. These chromatographic descriptors include both the retention mechanism and the peak shape on columns that reflect specific molecular interactions between solute and stationary and mobile phases and are characteristic of the molecular structure of BPs. The chromatographic peak shape such as the asymmetry and tailing factors had more influence on predicting the placental passage than the usual retention parameters. Furthermore, the QSAR model, having the best prediction capacity, was obtained with the chromatographic descriptors alone and met the criteria of internal and cross validation. These QSAR models are crucial for predicting the fetal exposure of this important class of emerging contaminants.
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Affiliation(s)
- Clémence A. Gély
- ToxAlim (Research Centre in Food Toxicology), National Research Institute for Agriculture, Food and Environment (INRAE), National Veterinay School of Toulouse (ENVT), University of Toulouse, 31076 Toulouse, France
- Therapeutic Innovations and Resistances (INTHERES), National Research Institute for Agriculture, Food and Environment (INRAE), National Veterinay School of Toulouse (ENVT), University of Toulouse, 31076 Toulouse, France
| | - Nicole Picard-Hagen
- ToxAlim (Research Centre in Food Toxicology), National Research Institute for Agriculture, Food and Environment (INRAE), National Veterinay School of Toulouse (ENVT), University of Toulouse, 31076 Toulouse, France
| | - Malika Chassan
- Therapeutic Innovations and Resistances (INTHERES), National Research Institute for Agriculture, Food and Environment (INRAE), National Veterinay School of Toulouse (ENVT), University of Toulouse, 31076 Toulouse, France
| | - Jean-Christophe Garrigues
- Molecular Interactions and Chemical and Photochemical Reactivity Laboratory (IMRCP), University of Toulouse, 31062 Toulouse, France
| | - Véronique Gayrard
- ToxAlim (Research Centre in Food Toxicology), National Research Institute for Agriculture, Food and Environment (INRAE), National Veterinay School of Toulouse (ENVT), University of Toulouse, 31076 Toulouse, France
| | - Marlène Z. Lacroix
- Therapeutic Innovations and Resistances (INTHERES), National Research Institute for Agriculture, Food and Environment (INRAE), National Veterinay School of Toulouse (ENVT), University of Toulouse, 31076 Toulouse, France
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Luconi M, Sogorb MA, Markert UR, Benfenati E, May T, Wolbank S, Roncaglioni A, Schmidt A, Straccia M, Tait S. Human-Based New Approach Methodologies in Developmental Toxicity Testing: A Step Ahead from the State of the Art with a Feto-Placental Organ-on-Chip Platform. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:15828. [PMID: 36497907 PMCID: PMC9737555 DOI: 10.3390/ijerph192315828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Developmental toxicity testing urgently requires the implementation of human-relevant new approach methodologies (NAMs) that better recapitulate the peculiar nature of human physiology during pregnancy, especially the placenta and the maternal/fetal interface, which represent a key stage for human lifelong health. Fit-for-purpose NAMs for the placental-fetal interface are desirable to improve the biological knowledge of environmental exposure at the molecular level and to reduce the high cost, time and ethical impact of animal studies. This article reviews the state of the art on the available in vitro (placental, fetal and amniotic cell-based systems) and in silico NAMs of human relevance for developmental toxicity testing purposes; in addition, we considered available Adverse Outcome Pathways related to developmental toxicity. The OECD TG 414 for the identification and assessment of deleterious effects of prenatal exposure to chemicals on developing organisms will be discussed to delineate the regulatory context and to better debate what is missing and needed in the context of the Developmental Origins of Health and Disease hypothesis to significantly improve this sector. Starting from this analysis, the development of a novel human feto-placental organ-on-chip platform will be introduced as an innovative future alternative tool for developmental toxicity testing, considering possible implementation and validation strategies to overcome the limitation of the current animal studies and NAMs available in regulatory toxicology and in the biomedical field.
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Affiliation(s)
- Michaela Luconi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy
- I.N.B.B. (Istituto Nazionale Biostrutture e Biosistemi), Viale Medaglie d’Oro 305, 00136 Rome, Italy
| | - Miguel A. Sogorb
- Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Avenida de la Universidad s/n, 03202 Elche, Spain
| | - Udo R. Markert
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany
| | - Emilio Benfenati
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy
| | - Tobias May
- InSCREENeX GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Susanne Wolbank
- Ludwig Boltzmann Institut for Traumatology, The Research Center in Cooperation with AUVA, Austrian Cluster for Tissue Regeneration, Donaueschingenstrasse 13, 1200 Vienna, Austria
| | - Alessandra Roncaglioni
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy
| | - Astrid Schmidt
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany
| | - Marco Straccia
- FRESCI by Science&Strategy SL, C/Roure Monjo 33, Vacarisses, 08233 Barcelona, Spain
| | - Sabrina Tait
- Centre for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
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Sobańska AW. Affinity of Compounds for Phosphatydylcholine-Based Immobilized Artificial Membrane-A Measure of Their Bioconcentration in Aquatic Organisms. MEMBRANES 2022; 12:membranes12111130. [PMID: 36422122 PMCID: PMC9692598 DOI: 10.3390/membranes12111130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 05/14/2023]
Abstract
The BCF (bioconcentration factor) of solutes in aquatic organisms is an important parameter because many undesired chemicals enter the ecosystem and affect the wildlife. Chromatographic retention factor log kwIAM obtained from immobilized artificial membrane (IAM) HPLC chromatography with buffered, aqueous mobile phases and calculated molecular descriptors obtained for a group of 120 structurally unrelated compounds were used to generate useful models of log BCF. It was established that log kwIAM obtained in the conditions described in this study is not sufficient as a sole predictor of bioconcentration. Simple, potentially useful models based on log kwIAM and a selection of readily available, calculated descriptors and accounting for over 88% of total variability were generated using multiple linear regression (MLR), partial least squares (PLS) regression and artificial neural networks (ANN). The models proposed in the study were tested on an external group of 120 compounds and on a group of 40 compounds with known experimental log BCF values. It was established that a relatively simple MLR model containing four independent variables leads to satisfying BCF predictions and is more intuitive than PLS or ANN models.
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Affiliation(s)
- Anna W Sobańska
- Department of Analytical Chemistry, Faculty of Pharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland
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12
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Chou CY, Lin P, Kim J, Wang SS, Wang CC, Tung CW. Ensemble learning for predicting ex vivo human placental barrier permeability. BMC Bioinformatics 2022; 22:629. [PMID: 36138350 PMCID: PMC9502578 DOI: 10.1186/s12859-022-04937-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background The placental barrier protects the fetus from exposure to some toxicants and is vital for drug development and risk assessment of environmental chemicals. However, in vivo experiments for assessing the placental barrier permeability of chemicals is not ethically acceptable. Although ex vivo placental perfusion methods provide good alternatives for the assessment of placental barrier permeability, the application to a large number of test chemicals could be time- and resource-consuming. Computational prediction models for ex vivo placental barrier permeability are therefore desirable. Methods A total of 87 chemicals and corresponding 1444 physicochemical properties were divided into training and test datasets. Three types of algorithms including linear regression, random forest, and ensemble models were applied to develop prediction models for ex vivo placental barrier permeability. Results Among the tested models, the ensemble model integrating the previous two methods performed best for predicting ex vivo human placental barrier permeability with correlation coefficients of 0.887 and 0.825 when considering the applicability domain. An additional test on seven newly curated chemicals from the literature showed a good correlation coefficient of 0.879 which was further improved to 0.921 by considering the variation of experiments. Conclusion In this study, the first valid predicting model for ex vivo human placental barrier permeability was developed following the OECD guideline. The model is expected to be useful for assessing the human placental barrier permeability and can be integrated with developmental toxicity prediction models for investigating the toxic effects of chemicals on the fetus. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04937-y.
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Affiliation(s)
- Che-Yu Chou
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
| | - Pinpin Lin
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
| | - Jongwoon Kim
- Chemical Safety Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Shan-Shan Wang
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
| | - Chia-Chi Wang
- Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan.
| | - Chun-Wei Tung
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan. .,Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County, Taiwan.
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13
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Montesinos-López OA, Montesinos-López A, Kismiantini, Roman-Gallardo A, Gardner K, Lillemo M, Fritsche-Neto R, Crossa J. Partial Least Squares Enhances Genomic Prediction of New Environments. Front Genet 2022; 13:920689. [PMID: 36313422 PMCID: PMC9608852 DOI: 10.3389/fgene.2022.920689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022] Open
Abstract
In plant breeding, the need to improve the prediction of future seasons or new locations and/or environments, also denoted as “leave one environment out,” is of paramount importance to increase the genetic gain in breeding programs and contribute to food and nutrition security worldwide. Genomic selection (GS) has the potential to increase the accuracy of future seasons or new locations because it is a predictive methodology. However, most statistical machine learning methods used for the task of predicting a new environment or season struggle to produce moderate or high prediction accuracies. For this reason, in this study we explore the use of the partial least squares (PLS) regression methodology for this specific task, and we benchmark its performance with the Bayesian Genomic Best Linear Unbiased Predictor (GBLUP) method. The benchmarking process was done with 14 real datasets. We found that in all datasets the PLS method outperformed the popular GBLUP method by margins between 0% (in the Indica data) and 228.28% (in the Disease data) across traits, environments, and types of predictors. Our results show great empirical evidence of the power of the PLS methodology for the prediction of future seasons or new environments.
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14
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van Hoogdalem MW, Wexelblatt SL, Akinbi HT, Vinks AA, Mizuno T. A review of pregnancy-induced changes in opioid pharmacokinetics, placental transfer, and fetal exposure: Towards fetomaternal physiologically-based pharmacokinetic modeling to improve the treatment of neonatal opioid withdrawal syndrome. Pharmacol Ther 2021; 234:108045. [PMID: 34813863 DOI: 10.1016/j.pharmthera.2021.108045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/29/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
Abstract
Physiologically-based pharmacokinetic (PBPK) modeling has emerged as a useful tool to study pharmacokinetics (PK) in special populations, such as pregnant women, fetuses, and newborns, where practical hurdles severely limit the study of drug behavior. PK in pregnant women is variable and everchanging, differing greatly from that in their nonpregnant female and male counterparts typically enrolled in clinical trials. PBPK models can accommodate pregnancy-induced physiological and metabolic changes, thereby providing mechanistic insights into maternal drug disposition and fetal exposure. Fueled by the soaring opioid epidemic in the United States, opioid use during pregnancy continues to rise, leading to an increased incidence of neonatal opioid withdrawal syndrome (NOWS). The severity of NOWS is influenced by a complex interplay of extrinsic and intrinsic factors, and varies substantially between newborns, but the extent of prenatal opioid exposure is likely the primary driver. Fetomaternal PBPK modeling is an attractive approach to predict in utero opioid exposure. To facilitate the development of fetomaternal PBPK models of opioids, this review provides a detailed overview of pregnancy-induced changes affecting the PK of commonly used opioids during gestation. Moreover, the placental transfer of these opioids is described, along with their disposition in the fetus. Lastly, the implementation of these factors into PBPK models is discussed. Fetomaternal PBPK modeling of opioids is expected to provide improved insights in fetal opioid exposure, which allows for prediction of postnatal NOWS severity, thereby opening the way for precision postnatal treatment of these vulnerable infants.
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Affiliation(s)
- Matthijs W van Hoogdalem
- Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, USA
| | - Scott L Wexelblatt
- Perinatal Institute, Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA; Center for Addiction Research, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Henry T Akinbi
- Perinatal Institute, Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Alexander A Vinks
- Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA; Center for Addiction Research, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Tomoyuki Mizuno
- Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA; Center for Addiction Research, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
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15
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Costa J, Mackay R, de Aguiar Greca SC, Corti A, Silva E, Karteris E, Ahluwalia A. The Role of the 3Rs for Understanding and Modeling the Human Placenta. J Clin Med 2021; 10:jcm10153444. [PMID: 34362227 PMCID: PMC8347836 DOI: 10.3390/jcm10153444] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Modeling the physiology of the human placenta is still a challenge, despite the great number of scientific advancements made in the field. Animal models cannot fully replicate the structure and function of the human placenta and pose ethical and financial hurdles. In addition, increasingly stricter animal welfare legislation worldwide is incentivizing the use of 3R (reduction, refinement, replacement) practices. What efforts have been made to develop alternative models for the placenta so far? How effective are they? How can we improve them to make them more predictive of human pathophysiology? To address these questions, this review aims at presenting and discussing the current models used to study phenomena at the placenta level: in vivo, ex vivo, in vitro and in silico. We describe the main achievements and opportunities for improvement of each type of model and critically assess their individual and collective impact on the pursuit of predictive studies of the placenta in line with the 3Rs and European legislation.
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Affiliation(s)
- Joana Costa
- Centro di Ricerca E.Piaggio, University of Pisa, 56126 Pisa, Italy; (J.C.); (A.C.)
| | - Ruth Mackay
- Centre for Genome Engineering and Maintenance, Department of Mechanical and Aerospace Engineering, Brunel University London, Uxbridge UB8 3PH, UK;
| | | | - Alessandro Corti
- Centro di Ricerca E.Piaggio, University of Pisa, 56126 Pisa, Italy; (J.C.); (A.C.)
- Department of Translational Medicine, University of Pisa, 56126 Pisa, Italy
| | - Elisabete Silva
- College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (S.-C.d.A.G.); (E.S.); (E.K.)
| | - Emmanouil Karteris
- College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (S.-C.d.A.G.); (E.S.); (E.K.)
| | - Arti Ahluwalia
- Centro di Ricerca E.Piaggio, University of Pisa, 56126 Pisa, Italy; (J.C.); (A.C.)
- Department of Information Engineering, University of Pisa, 56122 Pisa, Italy
- Interuniversity Centro for the Promotion of 3Rs Principles in Teaching and Research (Centro3R), Italy
- Correspondence:
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16
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Di Filippo JI, Bollini M, Cavasotto CN. A Machine Learning Model to Predict Drug Transfer Across the Human Placenta Barrier. Front Chem 2021; 9:714678. [PMID: 34354979 PMCID: PMC8329444 DOI: 10.3389/fchem.2021.714678] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/07/2021] [Indexed: 12/05/2022] Open
Abstract
The development of computational models for assessing the transfer of chemicals across the placental membrane would be of the utmost importance in drug discovery campaigns, in order to develop safe therapeutic options. We have developed a low-dimensional machine learning model capable of classifying compounds according to whether they can cross or not the placental barrier. To this aim, we compiled a database of 248 compounds with experimental information about their placental transfer, characterizing each compound with a set of ∼5.4 thousand descriptors, including physicochemical properties and structural features. We evaluated different machine learning classifiers and implemented a genetic algorithm, in a five cross validation scheme, to perform feature selection. The optimization was guided towards models displaying a low number of false positives (molecules that actually cross the placental barrier, but are predicted as not crossing it). A Linear Discriminant Analysis model trained with only four structural features resulted to be robust for this task, exhibiting only one false positive case across all testing folds. This model is expected to be useful in predicting placental drug transfer during pregnancy, and thus could be used as a filter for chemical libraries in virtual screening campaigns.
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Affiliation(s)
- Juan I Di Filippo
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Pilar, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
| | - Mariela Bollini
- Centro de Investigaciones en BioNanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Pilar, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
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17
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Wang CC, Lin P, Chou CY, Wang SS, Tung CW. Prediction of human fetal-maternal blood concentration ratio of chemicals. PeerJ 2020; 8:e9562. [PMID: 32742813 PMCID: PMC7380269 DOI: 10.7717/peerj.9562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background The measurement of human fetal-maternal blood concentration ratio (logFM) of chemicals is critical for the risk assessment of chemical-induced developmental toxicity. While a few in vitro and ex vivo experimental methods were developed for predicting logFM of chemicals, the obtained experimental results are not able to directly predict in vivo outcomes. Methods A total of 55 chemicals with logFM values representing in vivo fetal-maternal blood ratio were divided into training and test datasets. An interpretable linear regression model was developed along with feature selection methods. Cross-validation on training dataset and prediction on independent test dataset were conducted to validate the prediction model. Results This study presents the first valid quantitative structure-activity relationship model following the Organisation for Economic Co-operation and Development (OECD) guidelines based on multiple linear regression for predicting in vivo logFM values. The autocorrelation descriptor AATSC1c and information content descriptor ZMIC1 were identified as informative features for predicting logFM. After the adjustment of the applicability domain, the developed model performs well with correlation coefficients of 0.875, 0.850 and 0.847 for model fitting, leave-one-out cross-validation and independent test, respectively. The model is expected to be useful for assessing human transplacental exposure.
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Affiliation(s)
- Chia-Chi Wang
- Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Pinpin Lin
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
| | - Che-Yu Chou
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
| | - Shan-Shan Wang
- Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
| | - Chun-Wei Tung
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County, Taiwan.,Graduate Institute of Data Science, Taipei Medical University, Taipei, Taiwan
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18
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Tsanaktsidou E, Karavasili C, Zacharis CK, Fatouros DG, Markopoulou CK. Partial Least Square Model (PLS) as a Tool to Predict the Diffusion of Steroids Across Artificial Membranes. Molecules 2020; 25:molecules25061387. [PMID: 32197506 PMCID: PMC7144563 DOI: 10.3390/molecules25061387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022] Open
Abstract
One of the most challenging goals in modern pharmaceutical research is to develop models that can predict drugs’ behavior, particularly permeability in human tissues. Since the permeability is closely related to the molecular properties, numerous characteristics are necessary in order to develop a reliable predictive tool. The present study attempts to decode the permeability by correlating the apparent permeability coefficient (Papp) of 33 steroids with their properties (physicochemical and structural). The Papp of the molecules was determined by in vitro experiments and the results were plotted as Y variable on a Partial Least Squares (PLS) model, while 37 pharmacokinetic and structural properties were used as X descriptors. The developed model was subjected to internal validation and it tends to be robust with good predictive potential (R2Y = 0.902, RMSEE = 0.00265379, Q2Y = 0.722, RMSEP = 0.0077). Based on the results specific properties (logS, logP, logD, PSA and VDss) were proved to be more important than others in terms of drugs Papp. The models can be utilized to predict the permeability of a new candidate drug avoiding needless animal experiments, as well as time and material consuming experiments.
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Affiliation(s)
- Eleni Tsanaktsidou
- Laboratory of Pharmaceutical Analysis, Department of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.T.); (C.K.Z.)
| | - Christina Karavasili
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (C.K.); (D.G.F.)
| | - Constantinos K. Zacharis
- Laboratory of Pharmaceutical Analysis, Department of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.T.); (C.K.Z.)
| | - Dimitrios G. Fatouros
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (C.K.); (D.G.F.)
| | - Catherine K. Markopoulou
- Laboratory of Pharmaceutical Analysis, Department of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.T.); (C.K.Z.)
- Correspondence: ; Tel.: +30-231-099-7665
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19
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Ancuceanu R, Tamba B, Stoicescu CS, Dinu M. Use of QSAR Global Models and Molecular Docking for Developing New Inhibitors of c-src Tyrosine Kinase. Int J Mol Sci 2019; 21:ijms21010019. [PMID: 31861445 PMCID: PMC6981969 DOI: 10.3390/ijms21010019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
A prototype of a family of at least nine members, cellular Src tyrosine kinase is a therapeutically interesting target because its inhibition might be of interest not only in a number of malignancies, but also in a diverse array of conditions, from neurodegenerative pathologies to certain viral infections. Computational methods in drug discovery are considerably cheaper than conventional methods and offer opportunities of screening very large numbers of compounds in conditions that would be simply impossible within the wet lab experimental settings. We explored the use of global quantitative structure-activity relationship (QSAR) models and molecular ligand docking in the discovery of new c-src tyrosine kinase inhibitors. Using a dataset of 1038 compounds from ChEMBL database, we developed over 350 QSAR classification models. A total of 49 models with reasonably good performance were selected and the models were assembled by stacking with a simple majority vote and used for the virtual screening of over 100,000 compounds. A total of 744 compounds were predicted by at least 50% of the QSAR models as active, 147 compounds were within the applicability domain and predicted by at least 75% of the models to be active. The latter 147 compounds were submitted to molecular ligand docking using AutoDock Vina and LeDock, and 89 were predicted to be active based on the energy of binding.
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Affiliation(s)
- Robert Ancuceanu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania; (R.A.); (M.D.)
| | - Bogdan Tamba
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa, University of Medicine and Pharmacy of Iasi, 700115 Iasi, Romania
- Correspondence:
| | - Cristina Silvia Stoicescu
- Department of Chemical Thermodynamics, Institute of Physical Chemistry “Ilie Murgulescu”, 060021 Bucharest, Romania;
| | - Mihaela Dinu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania; (R.A.); (M.D.)
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20
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Codaccioni M, Bois F, Brochot C. Placental transfer of xenobiotics in pregnancy physiologically-based pharmacokinetic models: Structure and data. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2019.100111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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In Vitro Models for Studying Transport Across Epithelial Tissue Barriers. Ann Biomed Eng 2018; 47:1-21. [DOI: 10.1007/s10439-018-02124-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/28/2018] [Indexed: 12/16/2022]
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22
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Yang HF, Zhang XN, Li Y, Zhang YH, Xu Q, Wei DQ. Theoretical Studies of Intracellular Concentration of Micro-organisms' Metabolites. Sci Rep 2017; 7:9048. [PMID: 28831069 PMCID: PMC5567373 DOI: 10.1038/s41598-017-08793-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/13/2017] [Indexed: 02/03/2023] Open
Abstract
With the rapid growth of micro-organism metabolic networks, acquiring the intracellular concentration of microorganisms’ metabolites accurately in large-batch is critical to the development of metabolic engineering and synthetic biology. Complementary to the experimental methods, computational methods were used as effective assessing tools for the studies of intracellular concentrations of metabolites. In this study, the dataset of 130 metabolites from E. coli and S. cerevisiae with available experimental concentrations were utilized to develop a SVM model of the negative logarithm of the concentration (-logC). In this statistic model, in addition to common descriptors of molecular properties, two special types of descriptors including metabolic network topologic descriptors and metabolic pathway descriptors were included. All 1997 descriptors were finally reduced into 14 by variable selections including genetic algorithm (GA). The model was evaluated through internal validations by 10-fold and leave-one-out (LOO) cross-validation, as well as external validations by predicting -logC values of the test set. The developed SVM model is robust and has a strong predictive potential (n = 91, m = 14, R2 = 0.744, RMSE = 0.730, Q2 = 0.57; R2p = 0.59, RMSEp = 0.702, Q2p = 0.58). An effective tool could be provided by this analysis for the large-batch prediction of the intracellular concentrations of the micro-organisms’ metabolites.
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Affiliation(s)
- Hai-Feng Yang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Nan Zhang
- Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, and College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Yan Li
- Department of Chinese Traditional Medicine, Chongqing Medical University, Chongqing, China
| | - Yong-Hong Zhang
- Medicine Engineering Research Center, and College of Pharmacy, Chongqing Medical University, Chongqing, China.
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Risk of prenatal depression and stress treatment: alteration on serotonin system of offspring through exposure to Fluoxetine. Sci Rep 2016; 6:33822. [PMID: 27703173 PMCID: PMC5050550 DOI: 10.1038/srep33822] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/01/2016] [Indexed: 01/23/2023] Open
Abstract
Fluoxetine is widely used to treat depression, including depression in pregnant and postpartum women. Studies suggest that fluoxetine may have adverse effects on offspring, presumably through its action on various serotonin receptors (HTRs). However, definitive evidence and the underlying mechanisms are largely unavailable. As initial steps towards establishing a human cellular and animal model, we analyzed the expression patterns of several HTRs through the differentiation of human induced pluripotent stem (hiPS) cells into neuronal cells, and analyzed expression pattern in zebrafish embryos. Treatment of zebrafish embryos with fluoxetine significantly blocked the expression of multiple HTRs. Furthermore, fluoxetine gave rise to a change in neuropsychology. Embryos treated with fluoxetine continued to exhibit abnormal behavior upto 12 days post fertilization due to changes in HTRs. These findings support a possible long-term risk of serotonin pathway alteration, possibly resulting from the "placental drug transfer".
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