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Komura H, Watanabe R, Mizuguchi K. The Trends and Future Prospective of In Silico Models from the Viewpoint of ADME Evaluation in Drug Discovery. Pharmaceutics 2023; 15:2619. [PMID: 38004597 PMCID: PMC10675155 DOI: 10.3390/pharmaceutics15112619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Drug discovery and development are aimed at identifying new chemical molecular entities (NCEs) with desirable pharmacokinetic profiles for high therapeutic efficacy. The plasma concentrations of NCEs are a biomarker of their efficacy and are governed by pharmacokinetic processes such as absorption, distribution, metabolism, and excretion (ADME). Poor ADME properties of NCEs are a major cause of attrition in drug development. ADME screening is used to identify and optimize lead compounds in the drug discovery process. Computational models predicting ADME properties have been developed with evolving model-building technologies from a simplified relationship between ADME endpoints and physicochemical properties to machine learning, including support vector machines, random forests, and convolution neural networks. Recently, in the field of in silico ADME research, there has been a shift toward evaluating the in vivo parameters or plasma concentrations of NCEs instead of using predictive results to guide chemical structure design. Another research hotspot is the establishment of a computational prediction platform to strengthen academic drug discovery. Bioinformatics projects have produced a series of in silico ADME models using free software and open-access databases. In this review, we introduce prediction models for various ADME parameters and discuss the currently available academic drug discovery platforms.
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Affiliation(s)
- Hiroshi Komura
- University Research Administration Center, Osaka Metropolitan University, 1-2-7 Asahimachi, Abeno-ku, Osaka 545-0051, Osaka, Japan
| | - Reiko Watanabe
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Osaka, Japan; (R.W.); (K.M.)
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition (NIBIOHN), 3-17 Senrioka-shinmachi, Settu 566-0002, Osaka, Japan
| | - Kenji Mizuguchi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Osaka, Japan; (R.W.); (K.M.)
- Artificial Intelligence Centre for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition (NIBIOHN), 3-17 Senrioka-shinmachi, Settu 566-0002, Osaka, Japan
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2
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Cornelissen F, Markert G, Deutsch G, Antonara M, Faaij N, Bartelink I, Noske D, Vandertop WP, Bender A, Westerman BA. Explaining Blood-Brain Barrier Permeability of Small Molecules by Integrated Analysis of Different Transport Mechanisms. J Med Chem 2023; 66:7253-7267. [PMID: 37217193 PMCID: PMC10259449 DOI: 10.1021/acs.jmedchem.2c01824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 05/24/2023]
Abstract
The blood-brain barrier (BBB) represents a major obstacle to delivering drugs to the central nervous system (CNS), resulting in the lack of effective treatment for many CNS diseases including brain cancer. To accelerate CNS drug development, computational prediction models could save the time and effort needed for experimental evaluation. Here, we studied BBB permeability focusing on active transport (influx and efflux) as well as passive diffusion using previously published and self-curated data sets. We created prediction models based on physicochemical properties, molecular substructures, or their combination to understand which mechanisms contribute to BBB permeability. Our results show that features that predicted passive diffusion over membranes overlap with features that explain endothelial permeation of approved CNS-active drugs. We also identified physical properties and molecular substructures that positively or negatively predicted BBB transport. These findings provide guidance toward identifying BBB-permeable compounds by optimally matching physicochemical and molecular properties to BBB transport mechanisms.
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Affiliation(s)
- Fleur
M.G. Cornelissen
- Department
of Neurosurgery, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
| | - Greta Markert
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K.
| | - Ghislaine Deutsch
- Department
of Neurosurgery, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K.
| | - Maria Antonara
- Department
of Neurosurgery, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K.
| | - Noa Faaij
- Department
of Neurosurgery, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
| | - Imke Bartelink
- Department
of Pharmacy, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
| | - David Noske
- Department
of Neurosurgery, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
| | - W. Peter Vandertop
- Department
of Neurosurgery, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
| | - Andreas Bender
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K.
| | - Bart A. Westerman
- Department
of Neurosurgery, Amsterdam UMC, location VUMC, Cancer Center, Amsterdam 1105, AZ, the Netherlands
- Window
Consortium (www.window-consortium.org)
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3
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Al-Fakih AM, Algamal ZY, Qasim MK. An improved opposition-based crow search algorithm for biodegradable material classification. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:403-415. [PMID: 35469528 DOI: 10.1080/1062936x.2022.2064546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
The development of a reliable quantitative structure-activity relationship (QSAR) classification model with a small number of molecular descriptors is a crucial step in chemometrics. In this study, an improvement of crow search algorithm (CSA) is proposed by adapting the opposite-based learning (OBL) approach, which is named as OBL-CSA, to improve the exploration and exploitation capability of the CSA in quantitative structure-biodegradation relationship (QSBR) modelling of classifying the biodegradable materials. The results reveal that the performance of OBL-CSA not only manifest in improving the classification performance, but also in reduced computational time required to complete the process when compared to the standard CSA and other four optimization algorithms tested, which are the particle swarm algorithm (PSO), black hole algorithm (BHA), grey wolf algorithm (GWA), and whale optimization algorithm (WOA). In conclusion, the OBL-CSA could be a valuable resource in the classification of biodegradable materials.
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Affiliation(s)
- A M Al-Fakih
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia and Department of Chemistry, Faculty of Science, Sana'a University, Sana'a, Yemen
| | - Z Y Algamal
- Department of Statistics and Informatics, University of Mosul, Mosul, Iraq
| | - M K Qasim
- Department of General Science, University of Mosul, Mosul, Iraq
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4
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Chaparro D, Flores-Gaspar A, Alí-Torres J. Computational Design of Copper Ligands with Controlled Metal Chelating, Pharmacokinetics, and Redox Properties for Alzheimer's Disease. J Alzheimers Dis 2021; 82:S179-S193. [PMID: 34032611 DOI: 10.3233/jad-200911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Redox active metal cations, such as Cu2 +, have been related to induce amyloid plaques formation and oxidative stress, which are two of the key events in the development of Alzheimer's disease (AD) and others metal promoted neurodegenerative diseases. In these oxidative events, standard reduction potential (SRP) is an important property especially relevant in the reactive oxygen species formation. OBJECTIVE The SRP is not usually considered for the selection of drug candidates in anti-AD treatments. In this work, we present a computational protocol for the selection of multifunctional ligands with suitable metal chelating, pharmacokinetics, and redox properties. METHODS The filtering process is based on quantum chemical calculations and the use of in silico tools. Calculations of SRP were performed by using the M06-2X density functional and the isodesmic approach. Then, a virtual screening technique (VS) was used for similar structure search. RESULTS Protocol application allowed the assessment of chelating, drug likeness, and redox properties of copper ligands. Those molecules showing the best features were selected as molecular scaffolds for a VS procedure in order to obtain related compounds. After applying this process, we present a list of candidates with suitable properties to prevent the redox reactions mediated by copper(II) ion. CONCLUSION The protocol incorporates SRP in the filtering stage and can be effectively used to obtain a set of potential drug candidates for AD treatments.
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Affiliation(s)
- Diego Chaparro
- Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia.,Departamento de Química, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Areli Flores-Gaspar
- Departamento de Química, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Jorge Alí-Torres
- Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
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5
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Algamal ZY, Qasim MK, Lee MH, Ali HTM. QSAR model for predicting neuraminidase inhibitors of influenza A viruses (H1N1) based on adaptive grasshopper optimization algorithm. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:803-814. [PMID: 32938208 DOI: 10.1080/1062936x.2020.1818616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
High-dimensionality is one of the major problems which affect the quality of the quantitative structure-activity relationship (QSAR) modelling. Obtaining a reliable QSAR model with few descriptors is an essential procedure in chemometrics. The binary grasshopper optimization algorithm (BGOA) is a new meta-heuristic optimization algorithm, which has been used successfully to perform feature selection. In this paper, four new transfer functions were adapted to improve the exploration and exploitation capability of the BGOA in QSAR modelling of influenza A viruses (H1N1). The QSAR model with these new quadratic transfer functions was internally and externally validated based on MSEtrain, Y-randomization test, MSEtest, and the applicability domain (AD). The validation results indicate that the model is robust and not due to chance correlation. In addition, the results indicate that the descriptor selection and prediction performance of the QSAR model for training dataset outperform the other S-shaped and V-shaped transfer functions. QSAR model using quadratic transfer function shows the lowest MSEtrain. For the test dataset, proposed QSAR model shows lower value of MSEtest compared with the other methods, indicating its higher predictive ability. In conclusion, the results reveal that the proposed QSAR model is an efficient approach for modelling high-dimensional QSAR models and it is useful for the estimation of IC50 values of neuraminidase inhibitors that have not been experimentally tested.
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Affiliation(s)
- Z Y Algamal
- Department of Statistics and Informatics, University of Mosul , Mosul, Iraq
| | - M K Qasim
- Department of General Science, University of Mosul , Mosul, Iraq
| | - M H Lee
- Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia , Johor, Malaysia
| | - H T M Ali
- College of Computers and Information Technology, Nawroz University , Dahuk, Iraq
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6
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Patel M, Chilton ML, Sartini A, Gibson L, Barber C, Covey-Crump L, Przybylak KR, Cronin MTD, Madden JC. Assessment and Reproducibility of Quantitative Structure–Activity Relationship Models by the Nonexpert. J Chem Inf Model 2018; 58:673-682. [DOI: 10.1021/acs.jcim.7b00523] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mukesh Patel
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Martyn L. Chilton
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Andrea Sartini
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Laura Gibson
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Chris Barber
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Liz Covey-Crump
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, England
| | - Katarzyna R. Przybylak
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Mark T. D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Judith C. Madden
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
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7
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Modarres HP, Janmaleki M, Novin M, Saliba J, El-Hajj F, RezayatiCharan M, Seyfoori A, Sadabadi H, Vandal M, Nguyen MD, Hasan A, Sanati-Nezhad A. In vitro models and systems for evaluating the dynamics of drug delivery to the healthy and diseased brain. J Control Release 2018; 273:108-130. [PMID: 29378233 DOI: 10.1016/j.jconrel.2018.01.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/12/2022]
Abstract
The blood-brain barrier (BBB) plays a crucial role in maintaining brain homeostasis and transport of drugs to the brain. The conventional animal and Transwell BBB models along with emerging microfluidic-based BBB-on-chip systems have provided fundamental functionalities of the BBB and facilitated the testing of drug delivery to the brain tissue. However, developing biomimetic and predictive BBB models capable of reasonably mimicking essential characteristics of the BBB functions is still a challenge. In addition, detailed analysis of the dynamics of drug delivery to the healthy or diseased brain requires not only biomimetic BBB tissue models but also new systems capable of monitoring the BBB microenvironment and dynamics of barrier function and delivery mechanisms. This review provides a comprehensive overview of recent advances in microengineering of BBB models with different functional complexity and mimicking capability of healthy and diseased states. It also discusses new technologies that can make the next generation of biomimetic human BBBs containing integrated biosensors for real-time monitoring the tissue microenvironment and barrier function and correlating it with the dynamics of drug delivery. Such integrated system addresses important brain drug delivery questions related to the treatment of brain diseases. We further discuss how the combination of in vitro BBB systems, computational models and nanotechnology supports for characterization of the dynamics of drug delivery to the brain.
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Affiliation(s)
- Hassan Pezeshgi Modarres
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - Mohsen Janmaleki
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - Mana Novin
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - John Saliba
- Biomedical Engineering, Department of Mechanical Engineering, Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Fatima El-Hajj
- Biomedical Engineering, Department of Mechanical Engineering, Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Mahdi RezayatiCharan
- Breast Cancer Research Center (BCRC), ACECR, Tehran, Iran; School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Amir Seyfoori
- Breast Cancer Research Center (BCRC), ACECR, Tehran, Iran; School of Metallurgy and Materials Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Hamid Sadabadi
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada
| | - Milène Vandal
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Minh Dang Nguyen
- Departments of Clinical Neurosciences, Cell Biology and Anatomy, Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Anwarul Hasan
- Biomedical Engineering, Department of Mechanical Engineering, Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, 2713, Qatar
| | - Amir Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Canada; Center for BioEngineering Research and Education, University of Calgary, Calgary, Canada.
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8
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Algamal ZY, Lee MH. A new adaptive L1-norm for optimal descriptor selection of high-dimensional QSAR classification model for anti-hepatitis C virus activity of thiourea derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:75-90. [PMID: 28176549 DOI: 10.1080/1062936x.2017.1278618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/01/2017] [Indexed: 06/06/2023]
Abstract
A high-dimensional quantitative structure-activity relationship (QSAR) classification model typically contains a large number of irrelevant and redundant descriptors. In this paper, a new design of descriptor selection for the QSAR classification model estimation method is proposed by adding a new weight inside L1-norm. The experimental results of classifying the anti-hepatitis C virus activity of thiourea derivatives demonstrate that the proposed descriptor selection method in the QSAR classification model performs effectively and competitively compared with other existing penalized methods in terms of classification performance on both the training and the testing datasets. Moreover, it is noteworthy that the results obtained in terms of stability test and applicability domain provide a robust QSAR classification model. It is evident from the results that the developed QSAR classification model could conceivably be employed for further high-dimensional QSAR classification studies.
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Affiliation(s)
- Z Y Algamal
- a Department of Mathematical Sciences , Universiti Teknologi Malaysia , Skudai , Johor , Malaysia
| | - M H Lee
- a Department of Mathematical Sciences , Universiti Teknologi Malaysia , Skudai , Johor , Malaysia
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9
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Algamal ZY, Lee MH, Al-Fakih AM, Aziz M. High-dimensional QSAR modelling using penalized linear regression model with L1/2-norm. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:703-719. [PMID: 27628959 DOI: 10.1080/1062936x.2016.1228696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
In high-dimensional quantitative structure-activity relationship (QSAR) modelling, penalization methods have been a popular choice to simultaneously address molecular descriptor selection and QSAR model estimation. In this study, a penalized linear regression model with L1/2-norm is proposed. Furthermore, the local linear approximation algorithm is utilized to avoid the non-convexity of the proposed method. The potential applicability of the proposed method is tested on several benchmark data sets. Compared with other commonly used penalized methods, the proposed method can not only obtain the best predictive ability, but also provide an easily interpretable QSAR model. In addition, it is noteworthy that the results obtained in terms of applicability domain and Y-randomization test provide an efficient and a robust QSAR model. It is evident from the results that the proposed method may possibly be a promising penalized method in the field of computational chemistry research, especially when the number of molecular descriptors exceeds the number of compounds.
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Affiliation(s)
- Z Y Algamal
- a Department of Mathematical Sciences , Universiti Teknologi Malaysia , Johor , Malaysia
| | - M H Lee
- a Department of Mathematical Sciences , Universiti Teknologi Malaysia , Johor , Malaysia
| | - A M Al-Fakih
- b Department of Chemistry , Universiti Teknologi Malaysia , Johor , Malaysia
| | - M Aziz
- b Department of Chemistry , Universiti Teknologi Malaysia , Johor , Malaysia
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10
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Gupta S, Basant N, Mohan D, Singh KP. Room-temperature and temperature-dependent QSRR modelling for predicting the nitrate radical reaction rate constants of organic chemicals using ensemble learning methods. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:539-558. [PMID: 27385532 DOI: 10.1080/1062936x.2016.1199592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
Experimental determinations of the rate constants of the reaction of NO3 with a large number of organic chemicals are tedious, and time and resource intensive; and the development of computational methods has widely been advocated. In this study, we have developed room-temperature (298 K) and temperature-dependent quantitative structure-reactivity relationship (QSRR) models based on the ensemble learning approaches (decision tree forest (DTF) and decision treeboost (DTB)) for predicting the rate constant of the reaction of NO3 radicals with diverse organic chemicals, under OECD guidelines. Predictive powers of the developed models were established in terms of statistical coefficients. In the test phase, the QSRR models yielded a correlation (r(2)) of >0.94 between experimental and predicted rate constants. The applicability domains of the constructed models were determined. An attempt has been made to provide the mechanistic interpretation of the selected features for QSRR development. The proposed QSRR models outperformed the previous reports, and the temperature-dependent models offered a much wider applicability domain. This is the first report presenting a temperature-dependent QSRR model for predicting the nitrate radical reaction rate constant at different temperatures. The proposed models can be useful tools in predicting the reactivities of chemicals towards NO3 radicals in the atmosphere, hence, their persistence and exposure risk assessment.
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Affiliation(s)
- S Gupta
- a Environmental Chemistry Division , CSIR-Indian Institute of Toxicology Research , Lucknow , India
| | | | - D Mohan
- c School of Environmental Sciences, Jawaharlal Nehru University , New Delhi , India
| | - K P Singh
- a Environmental Chemistry Division , CSIR-Indian Institute of Toxicology Research , Lucknow , India
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Gupta S, Basant N, Singh KP. Predicting the hazardous dose of industrial chemicals in warm-blooded species using machine learning-based modelling approaches. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:479-498. [PMID: 26087353 DOI: 10.1080/1062936x.2015.1051584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The hazardous dose of a chemical (HD50) is an emerging and acceptable test statistic for the safety/risk assessment of chemicals. Since it is derived using the experimental toxicity values of the chemical in several test species, it is highly cumbersome, time and resource intensive. In this study, three machine learning-based QSARs were established for predicting the HD50 of chemicals in warm-blooded species following the OECD guidelines. A data set comprising HD50 values of 957 chemicals was used to develop SDT, DTF and DTB QSAR models. The diversity in chemical structures and nonlinearity in the data were verified. Several validation coefficients were derived to test the predictive and generalization abilities of the constructed QSARs. The chi-path descriptors were identified as the most influential in three QSARs. The DTF and DTB performed relatively better than SDT model and yielded r(2) values of 0.928 and 0.959 between the measured and predicted HD50 values in the complete data set. Substructure alerts responsible for the toxicity of the chemicals were identified. The results suggest the appropriateness of the developed QSARs for reliably predicting the HD50 values of chemicals, and they can be used for screening of new chemicals for their safety/risk assessment for regulatory purposes.
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Affiliation(s)
- S Gupta
- a Environmental Chemistry Division , CSIR-Indian Institute of Toxicology Research , Lucknow , India
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