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Li X, Zhang F, Zheng L, Guo J. Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134828. [PMID: 38876015 DOI: 10.1016/j.jhazmat.2024.134828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
The prediction of ecological toxicity plays an increasingly important role in modern society. However, the existing models often suffer from poor performance and limited predictive capabilities. In this study, we propose a novel approach for ecological toxicity assessment based on pre-trained models. By leveraging pre-training techniques and graph neural network models, we establish a highperformance predictive model. Furthermore, we incorporate a variational autoencoder to optimize the model, enabling simultaneous discrimination of toxicity to bees and molecular degradability. Additionally, despite the low similarity between the endogenous hormones in bees and the compounds in our dataset, our model confidently predicts that these hormones are non-toxic to bees, which further strengthens the credibility and accuracy of our model. We also discovered the negative correlation between the degradation and bee toxicity of compounds. In summary, this study presents an ecological toxicity assessment model with outstanding performance. The proposed model accurately predicts the toxicity of chemicals to bees and their degradability capabilities, offering valuable technical support to relevant fields.
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Affiliation(s)
- Xinkang Li
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangzhen Zheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China; Zelixir Biotech Company Ltd. Shanghai, China.
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao.
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2
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Velloso JPL, de Sá AGC, Pires DEV, Ascher DB. Engineering G protein-coupled receptors for stabilization. Protein Sci 2024; 33:e5000. [PMID: 38747401 PMCID: PMC11094779 DOI: 10.1002/pro.5000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/21/2024] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
G protein-coupled receptors (GPCRs) are one of the most important families of targets for drug discovery. One of the limiting steps in the study of GPCRs has been their stability, with significant and time-consuming protein engineering often used to stabilize GPCRs for structural characterization and drug screening. Unfortunately, computational methods developed using globular soluble proteins have translated poorly to the rational engineering of GPCRs. To fill this gap, we propose GPCR-tm, a novel and personalized structurally driven web-based machine learning tool to study the impacts of mutations on GPCR stability. We show that GPCR-tm performs as well as or better than alternative methods, and that it can accurately rank the stability changes of a wide range of mutations occurring in various types of class A GPCRs. GPCR-tm achieved Pearson's correlation coefficients of 0.74 and 0.46 on 10-fold cross-validation and blind test sets, respectively. We observed that the (structural) graph-based signatures were the most important set of features for predicting destabilizing mutations, which points out that these signatures properly describe the changes in the environment where the mutations occur. More specifically, GPCR-tm was able to accurately rank mutations based on their effect on protein stability, guiding their rational stabilization. GPCR-tm is available through a user-friendly web server at https://biosig.lab.uq.edu.au/gpcr_tm/.
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Affiliation(s)
- João Paulo L. Velloso
- School of Chemistry and Molecular Biosciences, The Australian Centre for EcogenomicsThe University of QueenslandBrisbaneQueenslandAustralia
- Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthThe University of MelbourneParkvilleVictoriaAustralia
| | - Alex G. C. de Sá
- School of Chemistry and Molecular Biosciences, The Australian Centre for EcogenomicsThe University of QueenslandBrisbaneQueenslandAustralia
- Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthThe University of MelbourneParkvilleVictoriaAustralia
| | - Douglas E. V. Pires
- School of Computing and Information SystemsThe University of MelbourneParkvilleVictoriaAustralia
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, The Australian Centre for EcogenomicsThe University of QueenslandBrisbaneQueenslandAustralia
- Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
- Baker Department of Cardiometabolic HealthThe University of MelbourneParkvilleVictoriaAustralia
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3
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Vaziri-Amjad S, Rahgosha R, Taherkhani A. Potential JAK2 Inhibitors from Selected Natural Compounds: A Promising Approach for Complementary Therapy in Cancer Patients. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2024; 2024:1114928. [PMID: 38706884 PMCID: PMC11068457 DOI: 10.1155/2024/1114928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 02/14/2024] [Accepted: 04/02/2024] [Indexed: 05/07/2024]
Abstract
Background Janus-activated kinase 2 (JAK2) plays a pivotal role in numerous essential biological processes, including proliferation, apoptosis, and metastasis in human cells. Prior studies have indicated that inhibiting JAK2 could be a promising strategy to mitigate cell proliferation and induce apoptosis in tumor cells. Objectives This study aimed to estimate the binding affinity of 79 herbal compounds, comprising 46 flavonoids, 21 anthraquinones, and 12 cinnamic acids, to the ATP-binding cleft of JAK2 to identify potential herbal inhibitors of JAK2. Methods The binding affinities between ligands and JAK2 were calculated utilizing AutoDock 4.0 software in conjunction with the Cygwin environment. Cross-validation was conducted using the Schrödinger tool. Molecular dynamics simulations were employed to evaluate the stability of docked poses for the most significant JAK2 inhibitors. Furthermore, the Discovery Studio Visualizer tool was utilized to elucidate interactions between the top-ranked JAK2 inhibitors and residues within the JAK2 ATP-binding site. Results Twelve flavonoids, two anthraquinones, and three cinnamic acids demonstrated substantial binding affinities to the protein kinase domain of the receptor, with a criterion of ΔGbinding < -10 kcal/mol. Among the studied flavonoids, anthraquinones, and cinnamic acid derivatives, orientin, chlorogenic acid, and pulmatin emerged as the most potent JAK2 inhibitors, exhibiting ΔGbinding scores of -14.49, -11.87, and -10.76 kcal/mol, respectively. Furthermore, the docked poses of orientin, pulmatin, and chlorogenic acid remained stable throughout 60 ns computer simulations. The average root mean square deviation values calculated for JAK2 when complexed with orientin, chlorogenic acid, and pulmatin were 2.04 Å, 2.06 Å, and 1.95 Å, respectively. Conclusion This study underscores the robust inhibitory potential of orientin, pulmatin, and chlorogenic acid against JAK2. The findings hold promise for the development of novel and effective drugs for cancer treatment.
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Affiliation(s)
- Samaneh Vaziri-Amjad
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Reza Rahgosha
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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4
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Myung Y, de Sá AGC, Ascher DB. Deep-PK: deep learning for small molecule pharmacokinetic and toxicity prediction. Nucleic Acids Res 2024:gkae254. [PMID: 38634808 DOI: 10.1093/nar/gkae254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/20/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
Evaluating pharmacokinetic properties of small molecules is considered a key feature in most drug development and high-throughput screening processes. Generally, pharmacokinetics, which represent the fate of drugs in the human body, are described from four perspectives: absorption, distribution, metabolism and excretion-all of which are closely related to a fifth perspective, toxicity (ADMET). Since obtaining ADMET data from in vitro, in vivo or pre-clinical stages is time consuming and expensive, many efforts have been made to predict ADMET properties via computational approaches. However, the majority of available methods are limited in their ability to provide pharmacokinetics and toxicity for diverse targets, ensure good overall accuracy, and offer ease of use, interpretability and extensibility for further optimizations. Here, we introduce Deep-PK, a deep learning-based pharmacokinetic and toxicity prediction, analysis and optimization platform. We applied graph neural networks and graph-based signatures as a graph-level feature to yield the best predictive performance across 73 endpoints, including 64 ADMET and 9 general properties. With these powerful models, Deep-PK supports molecular optimization and interpretation, aiding users in optimizing and understanding pharmacokinetics and toxicity for given input molecules. The Deep-PK is freely available at https://biosig.lab.uq.edu.au/deeppk/.
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Affiliation(s)
- Yoochan Myung
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland 4072, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Alex G C de Sá
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland 4072, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland 4072, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville, Victoria 3010, Australia
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5
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Di Stefano M, Galati S, Piazza L, Granchi C, Mancini S, Fratini F, Macchia M, Poli G, Tuccinardi T. VenomPred 2.0: A Novel In Silico Platform for an Extended and Human Interpretable Toxicological Profiling of Small Molecules. J Chem Inf Model 2024; 64:2275-2289. [PMID: 37676238 PMCID: PMC11005041 DOI: 10.1021/acs.jcim.3c00692] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 09/08/2023]
Abstract
The application of artificial intelligence and machine learning (ML) methods is becoming increasingly popular in computational toxicology and drug design; it is considered as a promising solution for assessing the safety profile of compounds, particularly in lead optimization and ADMET studies, and to meet the principles of the 3Rs, which calls for the replacement, reduction, and refinement of animal testing. In this context, we herein present the development of VenomPred 2.0 (http://www.mmvsl.it/wp/venompred2/), the new and improved version of our free of charge web tool for toxicological predictions, which now represents a powerful web-based platform for multifaceted and human-interpretable in silico toxicity profiling of chemicals. VenomPred 2.0 presents an extended set of toxicity endpoints (androgenicity, skin irritation, eye irritation, and acute oral toxicity, in addition to the already available carcinogenicity, mutagenicity, hepatotoxicity, and estrogenicity) that can be evaluated through an exhaustive consensus prediction strategy based on multiple ML models. Moreover, we also implemented a new utility based on the Shapley Additive exPlanations (SHAP) method that allows human interpretable toxicological profiling of small molecules, highlighting the features that strongly contribute to the toxicological predictions in order to derive structural toxicophores.
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Affiliation(s)
- Miriana Di Stefano
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Department
of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Salvatore Galati
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Lisa Piazza
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Carlotta Granchi
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Simone Mancini
- Department
of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124 Pisa, Italy
| | - Filippo Fratini
- Department
of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124 Pisa, Italy
| | - Marco Macchia
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Giulio Poli
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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6
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Velloso JPL, Kovacs AS, Pires DEV, Ascher DB. AI-driven GPCR analysis, engineering, and targeting. Curr Opin Pharmacol 2024; 74:102427. [PMID: 38219398 DOI: 10.1016/j.coph.2023.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
Abstract
This article investigates the role of recent advances in Artificial Intelligence (AI) to revolutionise the study of G protein-coupled receptors (GPCRs). AI has been applied to many areas of GPCR research, including the application of machine learning (ML) in GPCR classification, prediction of GPCR activation levels, modelling GPCR 3D structures and interactions, understanding G-protein selectivity, aiding elucidation of GPCRs structures, and drug design. Despite progress, challenges in predicting GPCR structures and addressing the complex nature of GPCRs remain, providing avenues for future research and development.
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Affiliation(s)
- João P L Velloso
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Aaron S Kovacs
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.
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7
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Abstract
The greatest challenge in drug discovery remains the high rate of attrition across the different phases of the process, which cost the industry billions of dollars every year. While all phases remain crucial to ensure pharmaceutical-level safety, quality, and efficacy of the end product, streamlining these efforts toward compounds with success potential is pivotal for a more efficient and cost-effective process. The use of artificial intelligence (AI) within the pharmaceutical industry aims at just this, and has applications in preclinical screening for biological activity, optimization of pharmacokinetic properties for improved drug formulation, early toxicity prediction which reduces attrition, and pre-emptively screening for genetic changes in the biological target to improve therapeutic longevity. Here, we present a series of in silico tools that address these applications in small molecule development and describe how they can be embedded within the current pharmaceutical development pipeline.
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Affiliation(s)
- Adam Serghini
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
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8
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Shaker ME, Goma HAM, Alsalahat I, Elkanzi NAA, Azouz AA, Abdel-Bakky MS, Ghoneim MM, Hazem SH, El-Mesery ME, Farouk A, Alzarea SI, Alsahli TG, Alotaibi NH, Musa A, Abdelgawad MA, Bakr RB. Design and construction of novel pyridine-pyrimidine hybrids as selective COX-2 suppressors: anti-inflammatory potential, ulcerogenic profile, molecular modeling and ADME/Tox studies. J Biomol Struct Dyn 2023:1-14. [PMID: 38153371 DOI: 10.1080/07391102.2023.2293257] [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: 05/10/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023]
Abstract
NSAIDs represent a mainstay in pain and inflammation suppression, and their actions are mainly based on inhibiting COX-1 and COX-2 enzymes.Due to the adverse effects of these drugs, especially on the stomach and heart, scientists efforts have been directed to manufacture selective COX-2 without cardiovascular side effects and with minimal effects on the stomach. The cardiovascular side effects are thought to be related to the chemical composition rather than mechanism of action of these drugs.Novel pyridopyrimidines, 9a-j, were prepared and their chemical structures were confirmed by NMR, mass and IR Spectra, and elemental analysis. The effect of the 9a-j compounds on COX-1 and COX-2 was assessed and it was found that 2-hydrazino-5-(4-methoxyphenyl)-7-phenyl-3H-pyrido[2,3-d)pyrimidin-4-one (9d) was the most potent COX-2 inhibitor (IC50 = 0.54 uM) compared to celecoxib (IC50 = 1.11 uM) with selectivity indices of 6.56 and 5.12, respectively.The in vivo inhibition of paw edema of novel compounds 9a-j was measured using carrageenan-induced paw edema method, and that 2-hydrazino-5-(4-methoxyphenyl)-7-phenyl-3H-pyrido[2,3-d)pyrimidin-4-one (9d) showed the best inhibitory activity in comparison with the other compounds and celecoxib.The gastroprotective effect of the potent derivatives 9d, 9e, 9f, 9 g and 9h was investigated. 2-Hydrazino-5-(4-methoxyphenyl)-7-phenyl-3H-pyrido[2,3-d)pyrimidin-4-one (9d) and 7-(chlorophenyl)-hydrazino-5-(4-methoxyphenyl)-3H-pyrido[2,3-d)pyrimidin-4-one (9e) showed ulcer indices comparable to celecoxib (1 and 0.5 vs 0.5, respectively). Docking studies were carried out and they confirmed the mechanistic action of the designed compoundsCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed E Shaker
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Hesham A M Goma
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Izzeddin Alsalahat
- UK Dementia Research Institute Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Nadia A A Elkanzi
- Department of Chemistry, College of Science, Jouf University, Sakaka, Saudi Arabia
| | - Amany A Azouz
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mohamed Sadek Abdel-Bakky
- Department of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Sara H Hazem
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohamed E El-Mesery
- Department of Biochemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Division of Biochemical Pharmacology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Amr Farouk
- Flavour and Aroma Chemistry Department, National Research Centre, Dokki, Cairo, Egypt
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Tariq G Alsahli
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Nasser Hadal Alotaibi
- Department of Clinical Pharmacy, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Arafa Musa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Rania B Bakr
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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9
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Hardianto A, Mardetia SS, Destiarani W, Budiman YP, Kurnia D, Mayanti T. Unveiling the Anti-Cancer Potential of Onoceranoid Triterpenes from Lansium domesticum Corr. cv. kokosan: An In Silico Study against Estrogen Receptor Alpha. Int J Mol Sci 2023; 24:15033. [PMID: 37834479 PMCID: PMC10573215 DOI: 10.3390/ijms241915033] [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: 08/23/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Breast cancer is a significant global concern, with tamoxifen, the standard treatment, raising long-term safety issues due to side effects. In this study, we evaluated the potential of five onoceranoid triterpenes from Lansium domesticum Corr. cv. kokosan against estrogen receptor alpha (ERα) using in silico techniques. Utilizing molecular docking, Lipinski's rule of five, in silico ADMET, and molecular dynamics simulations, we assessed the potency of five onoceranoid triterpenes against ERα. Molecular docking indicated competitive binding energies for these triterpenes relative to the active form of tamoxifen (4OHT) and estradiol, an ERα native ligand. Three triterpenes met drug-likeness criteria with favorable ADMET profiles. Notably, 2 demonstrated superior binding affinity in molecular dynamics simulations, outperforming estradiol, closely followed by 3 and 4. Hierarchical clustering on principal components (HCPC) and the spatial distribution of contact surface area (CSA) analyses suggest that these triterpenes, especially 2, may act as antagonist ligands akin to 4OHT. These findings highlight the potential of onoceranoid triterpenes in treating ERα-related breast cancer.
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Affiliation(s)
- Ari Hardianto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
| | - Sarah Syifa Mardetia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
| | - Wanda Destiarani
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 45363, West Java, Indonesia
| | - Yudha Prawira Budiman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
| | - Tri Mayanti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jatinangor 45363, West Java, Indonesia
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10
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He Y, Liu G, Hu S, Wang X, Jia J, Zhou H, Yan X. Implementing comprehensive machine learning models of multispecies toxicity assessment to improve regulation of organic compounds. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131942. [PMID: 37390684 DOI: 10.1016/j.jhazmat.2023.131942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/12/2023] [Accepted: 06/24/2023] [Indexed: 07/02/2023]
Abstract
Machine learning has made significant progress in assessing the risk associated with hazardous chemicals. However, most models were constructed by randomly selecting one algorithm and one toxicity endpoint towards single species, which may cause biased regulation of chemicals. In the present study, we implemented comprehensive prediction models involving multiple advanced machine learning and end-to-end deep learning to assess the aquatic toxicity of chemicals. The generated optimal models accurately unravel the quantitative structure-toxicity relationships, with the correlation coefficients of all training sets from 0.59 to 0.81 and of the test sets from 0.56 to 0.83. For each chemical, its ecological risk was determined from the toxicity information towards multiple species. The results also revealed the toxicity mechanism of chemicals was species sensitivity, and the high-level organisms were faced with more serious side effects from hazardous substances. The proposed approach was finally applied to screen over 16,000 compounds and identify high-risk chemicals. We believe that the current approach can provide a useful tool for predicting the toxicity of diverse organic chemicals and help regulatory authorities make more reasonable decisions.
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Affiliation(s)
- Ying He
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Guohong Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Agriculture and Biological Sciences, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Song Hu
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xiaohong Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jianbo Jia
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Hongyu Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Xiliang Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Agriculture and Biological Sciences, Qiannan Normal University for Nationalities, Duyun 558000, China.
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11
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Wu S, Pan Z, Li X, Wang Y, Tang J, Li H, Lu G, Li J, Feng Z, He Y, Liu X. Machine Learning Assisted Photothermal Conversion Efficiency Prediction of Anticancer Photothermal Agents. Chem Eng Sci 2023. [DOI: 10.1016/j.ces.2023.118619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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12
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CSM-Toxin: A Web-Server for Predicting Protein Toxicity. Pharmaceutics 2023; 15:pharmaceutics15020431. [PMID: 36839752 PMCID: PMC9966851 DOI: 10.3390/pharmaceutics15020431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
Biologics are one of the most rapidly expanding classes of therapeutics, but can be associated with a range of toxic properties. In small-molecule drug development, early identification of potential toxicity led to a significant reduction in clinical trial failures, however we currently lack robust qualitative rules or predictive tools for peptide- and protein-based biologics. To address this, we have manually curated the largest set of high-quality experimental data on peptide and protein toxicities, and developed CSM-Toxin, a novel in-silico protein toxicity classifier, which relies solely on the protein primary sequence. Our approach encodes the protein sequence information using a deep learning natural languages model to understand "biological" language, where residues are treated as words and protein sequences as sentences. The CSM-Toxin was able to accurately identify peptides and proteins with potential toxicity, achieving an MCC of up to 0.66 across both cross-validation and multiple non-redundant blind tests, outperforming other methods and highlighting the robust and generalisable performance of our model. We strongly believe the CSM-Toxin will serve as a valuable platform to minimise potential toxicity in the biologic development pipeline. Our method is freely available as an easy-to-use webserver.
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Zhou Y, Al‐Jarf R, Alavi A, Nguyen TB, Rodrigues CHM, Pires DEV, Ascher DB. kinCSM: Using graph-based signatures to predict small molecule CDK2 inhibitors. Protein Sci 2022; 31:e4453. [PMID: 36305769 PMCID: PMC9597374 DOI: 10.1002/pro.4453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
Protein phosphorylation acts as an essential on/off switch in many cellular signaling pathways. This has led to ongoing interest in targeting kinases for therapeutic intervention. Computer‐aided drug discovery has been proven a useful and cost‐effective approach for facilitating prioritization and enrichment of screening libraries, but limited effort has been devoted providing insights on what makes a potent kinase inhibitor. To fill this gap, here we developed kinCSM, an integrative computational tool capable of accurately identifying potent cyclin‐dependent kinase 2 (CDK2) inhibitors, quantitatively predicting CDK2 ligand–kinase inhibition constants (pKi) and classifying different types of inhibitors based on their favorable binding modes. kinCSM predictive models were built using supervised learning and leveraged the concept of graph‐based signatures to capture both physicochemical properties and geometry properties of small molecules. CDK2 inhibitors were accurately identified with Matthew's Correlation Coefficients (MCC) of up to 0.74, and inhibition constants predicted with Pearson's correlation of up to 0.76, both with consistent performances of 0.66 and 0.68 on a nonredundant blind test, respectively. kinCSM was also able to identify the potential type of inhibition for a given molecule, achieving MCC of up to 0.80 on cross‐validation and 0.73 on the blind test. Analyzing the molecular composition of revealed enriched chemical fragments in CDK2 inhibitors and different types of inhibitors, which provides insights into the molecular mechanisms behind ligand–kinase interactions. kinCSM will be an invaluable tool to guide future kinase drug discovery. To aid the fast and accurate screening of CDK2 inhibitors, kinCSM is freely available at https://biosig.lab.uq.edu.au/kin_csm/.
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Affiliation(s)
- Yunzhuo Zhou
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Raghad Al‐Jarf
- Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Azadeh Alavi
- Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Thanh Binh Nguyen
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Carlos H. M. Rodrigues
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Douglas E. V. Pires
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia,School of Computing and Information SystemsUniversity of MelbourneMelbourneVictoriaAustralia
| | - David B. Ascher
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
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