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Retnosari R, Ali AH, Zainalabidin S, Ugusman A, Oka N, Latip J. The recent discovery of a promising pharmacological scaffold derived from carvacrol: A review. Bioorg Med Chem Lett 2024; 109:129826. [PMID: 38830427 DOI: 10.1016/j.bmcl.2024.129826] [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: 12/11/2023] [Revised: 05/13/2024] [Accepted: 05/27/2024] [Indexed: 06/05/2024]
Abstract
Carvacrol, called CA, is a dynamic phytoconstituent characterized by a phenol ring abundantly sourced from various natural reservoirs. This versatile scaffold serves as a pivotal template for the design and synthesis of novel drug molecules, harboring promising biological activities. The active sites positioned at C-4, C-6, and the hydroxyl group (-OH) of CA offer fertile ground for creating potent drug candidates from a pharmacological standpoint. In this comprehensive review, we delve into diverse synthesis pathways and explore the biological activity of CA derivatives. We aim to illuminate the potential of these derivatives in discovering and developing efficacious treatments against a myriad of life-threatening diseases. By scrutinizing the structural modifications and pharmacophore placements that enhance the activity of CA derivatives, we aspire to inspire the innovation of novel therapeutics with heightened potency and effectiveness.
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Affiliation(s)
- Rini Retnosari
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia; International Joint Department of Materials Science and Engineering Between National University of Malaysia and Gifu University, Graduate School of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Department of Chemistry, Universitas Negeri Malang, Jl. Semarang No. 5 Malang, Indonesia
| | - Amatul Hamizah Ali
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Satirah Zainalabidin
- Programme of Biomedical Science, Centre for Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, 50300 Kuala Lumpur, Malaysia
| | - Azizah Ugusman
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Natsuhisa Oka
- International Joint Department of Materials Science and Engineering Between National University of Malaysia and Gifu University, Graduate School of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Jalifah Latip
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
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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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Shan L, Heusinkveld HJ, Paul KC, Hughes S, Darweesh SKL, Bloem BR, Homberg JR. Towards improved screening of toxins for Parkinson's risk. NPJ Parkinsons Dis 2023; 9:169. [PMID: 38114496 PMCID: PMC10730534 DOI: 10.1038/s41531-023-00615-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Parkinson's disease (PD) is a chronic, progressive and disabling neurodegenerative disorder. The prevalence of PD has risen considerably over the past decades. A growing body of evidence suggest that exposure to environmental toxins, including pesticides, solvents and heavy metals (collectively called toxins), is at least in part responsible for this rapid growth. It is worrying that the current screening procedures being applied internationally to test for possible neurotoxicity of specific compounds offer inadequate insights into the risk of developing PD in humans. Improved screening procedures are therefore urgently needed. Our review first substantiates current evidence on the relation between exposure to environmental toxins and the risk of developing PD. We subsequently propose to replace the current standard toxin screening by a well-controlled multi-tier toxin screening involving the following steps: in silico studies (tier 1) followed by in vitro tests (tier 2), aiming to prioritize agents with human relevant routes of exposure. More in depth studies can be undertaken in tier 3, with whole-organism (in)vertebrate models. Tier 4 has a dedicated focus on cell loss in the substantia nigra and on the presumed mechanisms of neurotoxicity in rodent models, which are required to confirm or refute the possible neurotoxicity of any individual compound. This improved screening procedure should not only evaluate new pesticides that seek access to the market, but also critically assess all pesticides that are being used today, acknowledging that none of these has ever been proven to be safe from a perspective of PD. Importantly, the improved screening procedures should not just assess the neurotoxic risk of isolated compounds, but should also specifically look at the cumulative risk conveyed by exposure to commonly used combinations of pesticides (cocktails). The worldwide implementation of such an improved screening procedure, would be an essential step for policy makers and governments to recognize PD-related environmental risk factors.
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Affiliation(s)
- Ling Shan
- Department Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, the Netherlands.
| | - Harm J Heusinkveld
- Centre for Health Protection, National Institute for Public Health and Environment (RIVM), Bilthoven, The Netherlands
| | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Samantha Hughes
- A-LIFE Amsterdam Institute for Life and Environment, Section Environmental Health and Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Sirwan K L Darweesh
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bastiaan R Bloem
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Judith R Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Callil-Soares PH, Biasi LCK, Pessoa Filho PDA. Effect of preprocessing and simulation parameters on the performance of molecular docking studies. J Mol Model 2023; 29:251. [PMID: 37452150 DOI: 10.1007/s00894-023-05637-x] [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: 02/13/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
CONTEXT Molecular docking is an important and rapid tool that provides a comprehensive view of different molecular mechanisms. It is often used to verify the binding interactions of many pairs of molecules and is much faster than more rigorous approaches. However, its application requires carefully preprocessing each molecule and selecting a series of simulation parameters, which is not always done correctly. We show how preprocessing and simulation parameters can positively or negatively impact molecular docking performance. For example, the inclusion of hydrogen atoms leads to better redocking scores, but molecular dynamics simulations must be performed under certain constraints; otherwise, it may worsen performance rather than improve it. This study clarifies the importance and influence of these different parameters in the simulation results. METHODS We analyzed the influence of different parameters on the predictive ability of molecular docking techniques using two software packages: AutoDock Vina and AutoDock-GPU. Thus, 90 receptor-ligand complexes were redocked, evaluating the root mean square deviation (RMSD) between the original position of the ligand (receptor-ligand complex obtained experimentally) and that obtained by the software for every analysis. We investigated the influence of hydrogen atoms (on the receptor and on the receptor-ligand complex), partial charges (QEq, QTPIE, EEM, EEM2015ha, MMFF94, Gasteiger-Marsili, and no charge), search boxes (size and exhaustiveness), ligand characteristics (size and number of torsions), and the use of molecular dynamics (of the receptor or the receptor-ligand complex) before docking analyses.
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Affiliation(s)
- Pedro Henrique Callil-Soares
- Chemical Engineering Department, Polytechnic School of the University of São Paulo, Av. Lineu Prestes, 580, São Paulo, 05508-000, Brazil
| | - Lilian Caroline Kramer Biasi
- Chemical Engineering Department, Polytechnic School of the University of São Paulo, Av. Lineu Prestes, 580, São Paulo, 05508-000, Brazil.
| | - Pedro de Alcântara Pessoa Filho
- Chemical Engineering Department, Polytechnic School of the University of São Paulo, Av. Lineu Prestes, 580, São Paulo, 05508-000, Brazil
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Dehydrovomifoliol Alleviates Nonalcoholic Fatty Liver Disease via the E2F1/AKT/mTOR Axis: Pharmacophore Modeling and Molecular Docking Study. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2023; 2023:9107598. [PMID: 36777627 PMCID: PMC9908351 DOI: 10.1155/2023/9107598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023]
Abstract
Objective Herbal medicine discovery is a complex and time-consuming process, while pharmacophore modeling and molecular docking methods enable simple and economic studies. The pharmacophore model provides an abstract description of essential intermolecular interactions between chemical structures, and the molecular docking technology can identify novel compounds of therapeutic interests and predict the ligand-target interaction at the molecular level. This study was based on the two methods to elucidate the mechanism of dehydrovomifoliol, an active ingredient extracted from Artemisia frigida willd, in nonalcoholic fatty liver disease (NAFLD). Methods Bioinformatics analysis was performed to screen target genes of dehydrovomifoliol in NAFLD treatment, which were thus intersected with NAFLD-related differentially expressed genes (DEGs) and NAFLD-related genes. Venn diagram was used to identify candidate DEGs. A pharmacophore model was then generated, and molecular docking was performed. A protein-protein interaction (PPI) network was constructed to identify core genes, which were evaluated using GO and the KEGG enrichment analyses. Results Seven target genes of dehydrovomifoliol in NAFLD treatment were screened out, namely E2F1, MERTK, SOX17, MMP9, SULT2A1, VEGFA, and BLVRA. The pharmacophore model and molecular docking of candidate DEGs and dehydrovomifoliol were successfully constructed. E2F1 was identified as a core gene of dehydrovomifoliol in NAFLD treatment. Further enrichment analysis indicated the regulatory role of E2F1 in fat metabolism was associated with the regulation of the AKT/mTOR signaling pathway. Conclusion Overall, this study illustrates the anti-NAFLD mechanism of dehydrovomifoliol, which could be a useful compound for developing novel drugs in the treatment of NAFLD.
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Creanza TM, Delre P, Ancona N, Lentini G, Saviano M, Mangiatordi GF. Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study. J Chem Inf Model 2021; 61:4758-4770. [PMID: 34506150 PMCID: PMC9282647 DOI: 10.1021/acs.jcim.1c00744] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Drug-induced blockade of the human
ether-à-go-go-related
gene (hERG) channel is today considered the main
cause of cardiotoxicity in postmarketing surveillance. Hence, several
ligand-based approaches were developed in the last years and are currently
employed in the early stages of a drug discovery process for in silico cardiac safety assessment of drug candidates.
Herein, we present the first structure-based classifiers able to discern hERG binders from nonbinders. LASSO regularized support
vector machines were applied to integrate docking scores and protein–ligand
interaction fingerprints. A total of 396 models were trained and validated
based on: (i) high-quality experimental bioactivity information returned
by 8337 curated compounds extracted from ChEMBL (version 25) and (ii)
structural predictor data. Molecular docking simulations were performed
using GLIDE and GOLD software programs and four different hERG structural models, namely, the recently published structures
obtained by cryoelectron microscopy (PDB codes: 5VA1 and 7CN1) and
two published homology models selected for comparison. Interestingly,
some classifiers return performances comparable to ligand-based models
in terms of area under the ROC curve (AUCMAX = 0.86 ±
0.01) and negative predictive values (NPVMAX = 0.81 ±
0.01), thus putting forward the herein proposed computational workflow
as a valuable tool for predicting hERG-related cardiotoxicity
without the limitations of ligand-based models, typically affected
by low interpretability and a limited applicability domain. From a
methodological point of view, our study represents the first example
of a successful integration of docking scores and protein–ligand
interaction fingerprints (IFs) through a support vector machine (SVM)
LASSO regularized strategy. Finally, the study highlights the importance
of using hERG structural models accounting for ligand-induced
fit effects and allowed us to select the best-performing protein conformation
(made available in the Supporting Information, SI) to be employed
for a reliable structure-based prediction of hERG-related cardiotoxicity.
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Affiliation(s)
- Teresa Maria Creanza
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Pietro Delre
- Chemistry Department, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.,CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
| | - Nicola Ancona
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Giovanni Lentini
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy
| | - Michele Saviano
- CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
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Akinola LK, Uzairu A, Shallangwa GA, Abechi SE. Theoretical study on endocrine disrupting effects of polychlorinated dibenzo‐
p
‐dioxins using molecular docking simulation. J Appl Toxicol 2020; 41:233-246. [DOI: 10.1002/jat.4039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Lukman K. Akinola
- Department of Chemistry Ahmadu Bello University Zaria Nigeria
- Department of Chemistry Bauchi State University Gadau Nigeria
| | - Adamu Uzairu
- Department of Chemistry Ahmadu Bello University Zaria Nigeria
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Schneider M, Pons JL, Labesse G, Bourguet W. In Silico Predictions of Endocrine Disruptors Properties. Endocrinology 2019; 160:2709-2716. [PMID: 31265055 PMCID: PMC6804484 DOI: 10.1210/en.2019-00382] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/26/2019] [Indexed: 01/12/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) are a broad class of molecules present in our environment that are suspected to cause adverse effects in the endocrine system by interfering with the synthesis, transport, degradation, or action of endogenous ligands. The characterization of the harmful interaction between environmental compounds and their potential cellular targets and the development of robust in vivo, in vitro, and in silico screening methods are important for assessment of the toxic potential of large numbers of chemicals. In this context, computer-aided technologies that will allow for activity prediction of endocrine disruptors and environmental risk assessments are being developed. These technologies must be able to cope with diverse data and connect chemistry at the atomic level with the biological activity at the cellular, organ, and organism levels. Quantitative structure-activity relationship methods became popular for toxicity issues. They correlate the chemical structure of compounds with biological activity through a number of molecular descriptors (e.g., molecular weight and parameters to account for hydrophobicity, topology, or electronic properties). Chemical structure analysis is a first step; however, modeling intermolecular interactions and cellular behavior will also be essential. The increasing number of three-dimensional crystal structures of EDCs' targets has provided a wealth of structural information that can be used to predict their interactions with EDCs using docking and scoring procedures. In the present review, we have described the various computer-assisted approaches that use ligands and targets properties to predict endocrine disruptor activities.
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Affiliation(s)
- Melanie Schneider
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Jean-Luc Pons
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Gilles Labesse
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
- Correspondence: Gilles Labesse, PhD, or William Bourguet, PhD, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France. E-mail: or
| | - William Bourguet
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
- Correspondence: Gilles Labesse, PhD, or William Bourguet, PhD, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France. E-mail: or
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