1
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Duan H, Lou C, Gu Y, Wang Y, Li W, Liu G, Tang Y. In Silico prediction of inhibitors for multiple transporters via machine learning methods. Mol Inform 2024; 43:e202300270. [PMID: 38235949 DOI: 10.1002/minf.202300270] [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: 10/07/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
Transporters play an indispensable role in facilitating the transport of nutrients, signaling molecules and the elimination of metabolites and toxins in human cells. Contemporary computational methods have been employed in the prediction of transporter inhibitors. However, these methods often focus on isolated endpoints, overlooking the interactions between transporters and lacking good interpretation. In this study, we integrated a comprehensive dataset and constructed models to assess the inhibitory effects on seven transporters. Both conventional machine learning and multi-task deep learning methods were employed. The results demonstrated that the MLT-GAT model achieved superior performance with an average AUC value of 0.882. It is noteworthy that our model excels not only in prediction performance but also in achieving robust interpretability, aided by GNN-Explainer. It provided valuable insights into transporter inhibition. The reliability of our model's predictions positioned it as a promising and valuable tool in the field of transporter inhibition research. Related data and code are available at https://gitee.com/wutiantian99/transporter_code.git.
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Affiliation(s)
- Hao Duan
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Chaofeng Lou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yaxin Gu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yimeng Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
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2
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Dudas B, Miteva MA. Computational and artificial intelligence-based approaches for drug metabolism and transport prediction. Trends Pharmacol Sci 2024; 45:39-55. [PMID: 38072723 DOI: 10.1016/j.tips.2023.11.001] [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: 08/02/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/07/2024]
Abstract
Drug metabolism and transport, orchestrated by drug-metabolizing enzymes (DMEs) and drug transporters (DTs), are implicated in drug-drug interactions (DDIs) and adverse drug reactions (ADRs). Reliable and precise predictions of DDIs and ADRs are critical in the early stages of drug development to reduce the rate of drug candidate failure. A variety of experimental and computational technologies have been developed to predict DDIs and ADRs. Recent artificial intelligence (AI) approaches offer new opportunities for better predicting and understanding the complex processes related to drug metabolism and transport. We summarize the role of major DMEs and DTs, and provide an overview of current progress in computational approaches for the prediction of drug metabolism, transport, and DDIs, with an emphasis on AI including machine learning (ML) and deep learning (DL) modeling.
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Affiliation(s)
- Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Maria A Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France.
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3
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Tran TTV, Tayara H, Chong KT. Recent Studies of Artificial Intelligence on In Silico Drug Absorption. J Chem Inf Model 2023; 63:6198-6211. [PMID: 37819031 DOI: 10.1021/acs.jcim.3c00960] [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] [Indexed: 10/13/2023]
Abstract
Absorption is an important area of research in pharmacochemistry and drug development, because the drug has to be absorbed before any drug effects can occur. Furthermore, the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profile of drugs can be directly and considerably altered by modulating factors affecting absorption. Many drugs in development fail because of poor absorption. The research and continuous efforts of researchers in recent years have brought many successes and promises in drug absorption property prediction, especially in silico, which helps to reduce the time and cost significantly for screening undesirable drug candidates. In this report, we explicitly provide an overview of recent in silico studies on predicting absorption properties, especially from 2019 to the present, using artificial intelligence. Additionally, we have collected and investigated public databases that support absorption prediction research. On those grounds, we also proposed the challenges and development directions of absorption prediction in the future. We hope this review can provide researchers with valuable guidelines on absorption prediction to facilitate the development of newer approaches in drug discovery.
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Affiliation(s)
- Thi Tuyet Van Tran
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Faculty of Information Technology, An Giang University, Long Xuyen 880000, Vietnam
- Vietnam National University, Ho Chi Minh City, Ho Chi Minh 700000, Vietnam
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Kil To Chong
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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4
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Kong X, Lin K, Wu G, Tao X, Zhai X, Lv L, Dong D, Zhu Y, Yang S. Machine Learning Techniques Applied to the Study of Drug Transporters. Molecules 2023; 28:5936. [PMID: 37630188 PMCID: PMC10459831 DOI: 10.3390/molecules28165936] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
With the advancement of computer technology, machine learning-based artificial intelligence technology has been increasingly integrated and applied in the fields of medicine, biology, and pharmacy, thereby facilitating their development. Transporters have important roles in influencing drug resistance, drug-drug interactions, and tissue-specific drug targeting. The investigation of drug transporter substrates and inhibitors is a crucial aspect of pharmaceutical development. However, long duration and high expenses pose significant challenges in the investigation of drug transporters. In this review, we discuss the present situation and challenges encountered in applying machine learning techniques to investigate drug transporters. The transporters involved include ABC transporters (P-gp, BCRP, MRPs, and BSEP) and SLC transporters (OAT, OATP, OCT, MATE1,2-K, and NET). The aim is to offer a point of reference for and assistance with the progression of drug transporter research, as well as the advancement of more efficient computer technology. Machine learning methods are valuable and attractive for helping with the study of drug transporter substrates and inhibitors, but continuous efforts are still needed to develop more accurate and reliable predictive models and to apply them in the screening process of drug development to improve efficiency and success rates.
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Affiliation(s)
- Xiaorui Kong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
| | - Kexin Lin
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
| | - Gaolei Wu
- Department of Pharmacy, Dalian Women and Children’s Medical Group, Dalian 116024, China;
| | - Xufeng Tao
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
| | - Xiaohan Zhai
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
| | - Linlin Lv
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
| | - Deshi Dong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
| | - Yanna Zhu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
| | - Shilei Yang
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (X.K.); (K.L.); (X.T.); (X.Z.); (L.L.); (D.D.)
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5
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Elbadawi M, Boulos JC, Dawood M, Zhou M, Gul W, ElSohly MA, Klauck SM, Efferth T. The Novel Artemisinin Dimer Isoniazide ELI-XXIII-98-2 Induces c-MYC Inhibition, DNA Damage, and Autophagy in Leukemia Cells. Pharmaceutics 2023; 15:1107. [PMID: 37111592 PMCID: PMC10144546 DOI: 10.3390/pharmaceutics15041107] [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: 02/15/2023] [Revised: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The proto-oncogenic transcription factor c-MYC plays a pivotal role in the development of tumorigenesis, cellular proliferation, and the control of cell death. Its expression is frequently altered in many cancer types, including hematological malignancies such as leukemia. The dimer isoniazide ELI-XXIII-98-2 is a derivative of the natural product artemisinin, with two artemisinin molecules and an isoniazide moiety as a linker in between them. In this study, we aimed to study the anticancer activity and the molecular mechanisms of this dimer molecule in drug-sensitive CCRF-CEM leukemia cells and their corresponding multidrug-resistant CEM/ADR5000 sub-line. The growth inhibitory activity was studied using the resazurin assay. To reveal the molecular mechanisms underlying the growth inhibitory activity, we performed in silico molecular docking, followed by several in vitro approaches such as the MYC reporter assay, microscale thermophoresis, microarray analyses, immunoblotting, qPCR, and comet assay. The artemisinin dimer isoniazide showed a potent growth inhibitory activity in CCRF-CEM but a 12-fold cross-resistance in multidrug-resistant CEM/ADR5000 cells. The molecular docking of artemisinin dimer isoniazide with c-MYC revealed a good binding (lowest binding energy of -9.84 ± 0.3 kcal/mol) and a predicted inhibition constant (pKi) of 66.46 ± 29.5 nM, which was confirmed by microscale thermophoresis and MYC reporter cell assays. Furthermore, c-MYC expression was downregulated by this compound in microarray hybridization and Western blotting analyses. Finally, the artemisinin dimer isoniazide modulated the expression of autophagy markers (LC3B and p62) and the DNA damage marker pH2AX, indicating the stimulation of both autophagy and DNA damage, respectively. Additionally, DNA double-strand breaks were observed in the alkaline comet assay. DNA damage, apoptosis, and autophagy induction could be attributed to the inhibition of c-MYC by ELI-XXIII-98-2.
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Affiliation(s)
- Mohamed Elbadawi
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, 55128 Mainz, Germany
| | - Joelle C. Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, 55128 Mainz, Germany
| | - Mona Dawood
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, 55128 Mainz, Germany
- Department of Molecular Biology, Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum 12702, Sudan
| | - Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, 55128 Mainz, Germany
| | - Waseem Gul
- ElSohly Laboratories, Inc., 5 Industrial Park Drive, Oxford, MS 38655, USA
| | - Mahmoud A. ElSohly
- ElSohly Laboratories, Inc., 5 Industrial Park Drive, Oxford, MS 38655, USA
| | - Sabine M. Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, 55128 Mainz, Germany
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6
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Kumar M, Nguyen TPN, Kaur J, Singh TG, Soni D, Singh R, Kumar P. Opportunities and challenges in application of artificial intelligence in pharmacology. Pharmacol Rep 2023; 75:3-18. [PMID: 36624355 PMCID: PMC9838466 DOI: 10.1007/s43440-022-00445-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/11/2023]
Abstract
Artificial intelligence (AI) is a machine science that can mimic human behaviour like intelligent analysis of data. AI functions with specialized algorithms and integrates with deep and machine learning. Living in the digital world can generate a huge amount of medical data every day. Therefore, we need an automated and reliable evaluation tool that can make decisions more accurately and faster. Machine learning has the potential to learn, understand and analyse the data used in healthcare systems. In the last few years, AI is known to be employed in various fields in pharmaceutical science especially in pharmacological research. It helps in the analysis of preclinical (laboratory animals) and clinical (in human) trial data. AI also plays important role in various processes such as drug discovery/manufacturing, diagnosis of big data for disease identification, personalized treatment, clinical trial research, radiotherapy, surgical robotics, smart electronic health records, and epidemic outbreak prediction. Moreover, AI has been used in the evaluation of biomarkers and diseases. In this review, we explain various models and general processes of machine learning and their role in pharmacological science. Therefore, AI with deep learning and machine learning could be relevant in pharmacological research.
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Affiliation(s)
- Mandeep Kumar
- Department of Pharmacy, Unit of Pharmacology and Toxicology, University of Genoa, Genoa, Italy
| | - T P Nhung Nguyen
- Department of Pharmacy, Unit of Pharmacology and Toxicology, University of Genoa, Genoa, Italy
- Department of Pharmacy, Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Jasleen Kaur
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Lucknow, Uttar Pradesh, 226002, India
| | | | - Divya Soni
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Randhir Singh
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India.
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7
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Puxeddu M, Wu J, Bai R, D’Ambrosio M, Nalli M, Coluccia A, Manetto S, Ciogli A, Masci D, Urbani A, Fionda C, Coni S, Bordone R, Canettieri G, Bigogno C, Dondio G, Hamel E, Liu T, Silvestri R, La Regina G. Induction of Ferroptosis in Glioblastoma and Ovarian Cancers by a New Pyrrole Tubulin Assembly Inhibitor. J Med Chem 2022; 65:15805-15818. [PMID: 36395526 PMCID: PMC9743090 DOI: 10.1021/acs.jmedchem.2c01457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We synthesized new aroyl diheterocyclic pyrrole (ARDHEP) 15 that exhibited the hallmarks of ferroptosis. Compound 15 strongly inhibited U-87 MG, OVCAR-3, and MCF-7 cancer cells, induced an increase of cleaved PARP, but was not toxic for normal human primary T lymphocytes at 0.1 μM. Analysis of the levels of lactoperoxidase, malondialdehyde, lactic acid, total glutathione, and ATP suggested that the in vivo inhibition of cancer cell proliferation by 15 went through stimulation of oxidative stress injury and Fe2+ accumulation. Quantitative polymerase chain reaction analysis of the mRNA expression in U-87 MG and SKOV-3 tumor tissues from 15-treated mice showed the presence of Ptgs2/Nfe2l2/Sat1/Akr1c1/Gpx4 genes correlated with ferroptosis in both groups. Immunofluorescence staining revealed significantly lower expressions of proteins Ki67, CD31, and ferroptosis negative regulation proteins glutathione peroxidase 4 (GPX4) and FTH1. Compound 15 was found to be metabolically stable when incubated with human liver microsomes.
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Affiliation(s)
- Michela Puxeddu
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy
| | - Jianchao Wu
- Shanghai
Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, 200031Shanghai, China
| | - Ruoli Bai
- Molecular
Pharmacology Branch, Developmental Therapeutics Program, Division
of Cancer Treatment and Diagnosis, Frederick National Laboratory for
Cancer Research, National Cancer Institute,
National Institutes of Health, Frederick, Maryland21702, United States
| | - Michele D’Ambrosio
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy
| | - Marianna Nalli
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy
| | - Antonio Coluccia
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy
| | - Simone Manetto
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy
| | - Alessia Ciogli
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy
| | - Domiziana Masci
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, 00168Rome, Italy
| | - Andrea Urbani
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, 00168Rome, Italy
| | - Cinzia Fionda
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Molecular Medicine, Sapienza
University of Rome, Viale Regina Elena 291, 00161Rome, Italy
| | - Sonia Coni
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Molecular Medicine, Sapienza
University of Rome, Viale Regina Elena 291, 00161Rome, Italy
| | - Rosa Bordone
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Molecular Medicine, Sapienza
University of Rome, Viale Regina Elena 291, 00161Rome, Italy
| | - Gianluca Canettieri
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Molecular Medicine, Sapienza
University of Rome, Viale Regina Elena 291, 00161Rome, Italy
| | - Chiara Bigogno
- Aphad
SrL, Via della Resistenza
65, 20090Buccinasco, Italy
| | - Giulio Dondio
- Aphad
SrL, Via della Resistenza
65, 20090Buccinasco, Italy
| | - Ernest Hamel
- Molecular
Pharmacology Branch, Developmental Therapeutics Program, Division
of Cancer Treatment and Diagnosis, Frederick National Laboratory for
Cancer Research, National Cancer Institute,
National Institutes of Health, Frederick, Maryland21702, United States
| | - Te Liu
- Shanghai
Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, 200031Shanghai, China,
| | - Romano Silvestri
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy,
| | - Giuseppe La Regina
- Laboratory
Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185Rome, Italy,
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8
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Mora Lagares L, Novič M. Recent Advances on P-Glycoprotein (ABCB1) Transporter Modelling with In Silico Methods. Int J Mol Sci 2022; 23:ijms232314804. [PMID: 36499131 PMCID: PMC9740644 DOI: 10.3390/ijms232314804] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/14/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
ABC transporters play a critical role in both drug bioavailability and toxicity, and with the discovery of the P-glycoprotein (P-gp), this became even more evident, as it plays an important role in preventing intracellular accumulation of toxic compounds. Over the past 30 years, intensive studies have been conducted to find new therapeutic molecules to reverse the phenomenon of multidrug resistance (MDR) ), that research has found is often associated with overexpression of P-gp, the most extensively studied drug efflux transporter; in MDR, therapeutic drugs are prevented from reaching their targets due to active efflux from the cell. The development of P-gp inhibitors is recognized as a good way to reverse this type of MDR, which has been the subject of extensive studies over the past few decades. Despite the progress made, no effective P-gp inhibitors to reverse multidrug resistance are yet on the market, mainly because of their toxic effects. Computational studies can accelerate this process, and in silico models such as QSAR models that predict the activity of compounds associated with P-gp (or analogous transporters) are of great value in the early stages of drug development, along with molecular modelling methods, which provide a way to explain how these molecules interact with the ABC transporter. This review highlights recent advances in computational P-gp research, spanning the last five years to 2022. Particular attention is given to the use of machine-learning approaches, drug-transporter interactions, and recent discoveries of potential P-gp inhibitors that could act as modulators of multidrug resistance.
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Affiliation(s)
- Liadys Mora Lagares
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-1-4760-438 (L.M.L.); +386-1-4760-253 (M.N.)
| | - Marjana Novič
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-1-4760-438 (L.M.L.); +386-1-4760-253 (M.N.)
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9
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Feng Y, Cheng X, Wu S, Mani Saravanan K, Liu W. Hybrid drug-screening strategy identifies potential SARS-CoV-2 cell-entry inhibitors targeting human transmembrane serine protease. Struct Chem 2022; 33:1503-1515. [PMID: 35571866 PMCID: PMC9091140 DOI: 10.1007/s11224-022-01960-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022]
Abstract
The spread of coronavirus infectious disease (COVID-19) is associated with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has risked public health more than any other infectious disease. Researchers around the globe use multiple approaches to identify an effective approved drug (drug repurposing) that treats viral infections. Most of the drug repurposing approaches target spike protein or main protease. Here we use transmembrane serine protease 2 (TMPRSS2) as a target that can prevent the virus entry into the cell by interacting with the surface receptors. By hypothesizing that the TMPRSS2 binders may help prevent the virus entry into the cell, we performed a systematic drug screening over the current approved drug database. Furthermore, we screened the Enamine REAL fragments dataset against the TMPRSS2 and presented nine potential drug-like compounds that give us clues about which kinds of groups the pocket prefers to bind, aiding future structure-based drug design for COVID-19. Also, we employ molecular dynamics simulations, binding free energy calculations, and well-tempered metadynamics to validate the obtained candidate drug and fragment list. Our results suggested three potential FDA-approved drugs against human TMPRSS2 as a target. These findings may pave the way for more drugs to be exposed to TMPRSS2, and testing the efficacy of these drugs with biochemical experiments will help improve COVID-19 treatment. Supplementary information The online version contains supplementary material available at 10.1007/s11224-022-01960-w.
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Affiliation(s)
- Yufei Feng
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048 Guangdong Province China
| | - Xiaoning Cheng
- Central People’s Hospital of Zhanjiang, Zhanjiang, 524045 Guangdong Province China
| | - Shuilong Wu
- Central People’s Hospital of Zhanjiang, Zhanjiang, 524045 Guangdong Province China
| | - Konda Mani Saravanan
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu 600073 India
| | - Wenxin Liu
- Central People’s Hospital of Zhanjiang, Zhanjiang, 524045 Guangdong Province China
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10
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Gorostiola González M, Janssen APA, IJzerman AP, Heitman LH, van Westen GJP. Oncological drug discovery: AI meets structure-based computational research. Drug Discov Today 2022; 27:1661-1670. [PMID: 35301149 DOI: 10.1016/j.drudis.2022.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 01/22/2022] [Accepted: 03/09/2022] [Indexed: 02/08/2023]
Abstract
The integration of machine learning and structure-based methods has proven valuable in the past as a way to prioritize targets and compounds in early drug discovery. In oncological research, these methods can be highly beneficial in addressing the diversity of neoplastic diseases portrayed by the different hallmarks of cancer. Here, we review six use case scenarios for integrated computational methods, namely driver prediction, computational mutagenesis, (off)-target prediction, binding site prediction, virtual screening, and allosteric modulation analysis. We address the heterogeneity of integration approaches and individual methods, while acknowledging their current limitations and highlighting their potential to bring drugs for personalized oncological therapies to the market faster.
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Affiliation(s)
- Marina Gorostiola González
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Antonius P A Janssen
- Oncode Institute, Utrecht, The Netherlands; Molecular Physiology, Leiden Institute of Chemistry, Leiden University, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Gerard J P van Westen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands.
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11
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Malhotra H, Kumar A, Afaq Y. Molecular docking analysis of FDA approved drugs with the glycoprotein from Junin and Machupo viruses. Bioinformation 2022; 18:119-126. [PMID: 36420432 PMCID: PMC9649494 DOI: 10.6026/97320630018119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/03/2022] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
Arenaviruses, Junin and Machupo are pathogenic viruses in regions of South America including Argentina and Bolivia causing haemorrhagic fever among humans. They have been transmitted to humans through mouse causing chronic illness with high mortality. Therefore, it is of interest to acquittance the molecular docking analysis data of FDA approved drugs with the glycoprotein from Junin and Machupo viruses for consideration in drug discovery. Thus, we report the optimal binding features of MK-3207 and Dihydro ergotamine with the protein target for further validation and consideration.
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Affiliation(s)
- Himani Malhotra
- Department of Biotechnology, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, INDIA - 144411
| | - Arvind Kumar
- Department of Computer Science, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, INDIA - 144411
| | - Yasir Afaq
- Department of Biochemistry, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab, INDIA - 144411
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12
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Pavan M, Bassani D, Bolcato G, Bissaro M, Sturles M, Moro S. Computational strategies to identify new drug candidates against neuroinflammation. Curr Med Chem 2022; 29:4756-4775. [PMID: 35135446 DOI: 10.2174/0929867329666220208095122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/22/2022]
Abstract
The even more increasing application of computational approaches in these last decades has deeply modified the process of discovery and commercialization of new therapeutic entities. This is especially true in the field of neuroinflammation, in which both the peculiar anatomical localization and the presence of the blood-brain barrier makeit mandatory to finely tune the candidates' physicochemical properties from the early stages of the discovery pipeline. The aim of this review is therefore to provide a general overview to the readers about the topic of neuroinflammation, together with the most common computational strategies that can be exploited to discover and design small molecules controlling neuroinflammation, especially those based on the knowledge of the three-dimensional structure of the biological targets of therapeutic interest. The techniques used to describe the molecular recognition mechanisms, such as molecular docking and molecular dynamics, will therefore be eviscerated, highlighting their advantages and their limitations. Finally, we report several case studies in which computational methods have been applied in drug discovery on neuroinflammation, focusing on the last decade's research.
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Affiliation(s)
- Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giovanni Bolcato
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Maicol Bissaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Mattia Sturles
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
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13
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Rathod S, Desai H, Patil R, Sarolia J. Non-ionic Surfactants as a P-Glycoprotein(P-gp) Efflux Inhibitor for Optimal Drug Delivery-A Concise Outlook. AAPS PharmSciTech 2022; 23:55. [PMID: 35043278 DOI: 10.1208/s12249-022-02211-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Significant research efforts have been devoted to unraveling the mystery of P-glycoprotein(P-gp) in drug delivery applications. The efflux membrane transporter P-gp is widely distributed in the body and accountable for restricting drug absorption and bioavailability. For these reasons, it is the primary cause of developing multidrug resistance (MDR) in most drug delivery applications. Therefore, P-gp inhibitors must be explored to address MDR and the low bioavailability of therapeutic substrates. Several experimental models in kinetics and dynamic studies identified the sensitivity of drug molecules and excipients as a P-gp inhibitor. In this review, we aimed to emphasize nonionic surface-active agents for effective reversal of P-gp inhibition. As it is inert, non-toxic, noncharged, and quickly reaching the cytosolic lipid membrane (the point of contact with P-gp efflux protein) enables it to be more efficient as P-gp inhibitors. Moreover, nonionic surfactant improves drug absorption and bioavailability through the various mechanism, involving (i) association of drug with surfactant improves solubilization, facilitating its cell penetration and absorption; (ii) weakening the lateral membrane packing density, facilitating the passive drug influx; and (iii) inhibition of the ATP binding cassette of transporter P-glycoprotein. The application of nonionic surfactant as P-gp inhibitors is well established and supported by various experiments. Altogether, herein, we have primarily focused on various nonionic surfactants and their development strategies to conquer the MDR-causing effects of P-gp efflux protein in drug delivery. Graphical Abstract.
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14
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Kadioglu O, Saeed M, Greten HJ, Efferth T. Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Comput Biol Med 2021; 133:104359. [PMID: 33845270 DOI: 10.2471/blt.20.255943] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 05/22/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a major threat worldwide due to its fast spreading. As yet, there are no established drugs available. Speeding up drug discovery is urgently required. We applied a workflow of combined in silico methods (virtual drug screening, molecular docking and supervised machine learning algorithms) to identify novel drug candidates against COVID-19. We constructed chemical libraries consisting of FDA-approved drugs for drug repositioning and of natural compound datasets from literature mining and the ZINC database to select compounds interacting with SARS-CoV-2 target proteins (spike protein, nucleocapsid protein, and 2'-o-ribose methyltransferase). Supported by the supercomputer MOGON, candidate compounds were predicted as presumable SARS-CoV-2 inhibitors. Interestingly, several approved drugs against hepatitis C virus (HCV), another enveloped (-) ssRNA virus (paritaprevir, simeprevir and velpatasvir) as well as drugs against transmissible diseases, against cancer, or other diseases were identified as candidates against SARS-CoV-2. This result is supported by reports that anti-HCV compounds are also active against Middle East Respiratory Virus Syndrome (MERS) coronavirus. The candidate compounds identified by us may help to speed up the drug development against SARS-CoV-2.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Mohamed Saeed
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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15
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Kadioglu O, Klauck SM, Fleischer E, Shan L, Efferth T. Selection of safe artemisinin derivatives using a machine learning-based cardiotoxicity platform and in vitro and in vivo validation. Arch Toxicol 2021; 95:2485-2495. [PMID: 34021777 PMCID: PMC8241674 DOI: 10.1007/s00204-021-03058-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/21/2021] [Indexed: 12/21/2022]
Abstract
The majority of drug candidates fails the approval phase due to unwanted toxicities and side effects. Establishment of an effective toxicity prediction platform is of utmost importance, to increase the efficiency of the drug discovery process. For this purpose, we developed a toxicity prediction platform with machine-learning strategies. Cardiotoxicity prediction was performed by establishing a model with five parameters (arrhythmia, cardiac failure, heart block, hypertension, myocardial infarction) and additional toxicity predictions such as hepatotoxicity, reproductive toxicity, mutagenicity, and tumorigenicity are performed by using Data Warrior and Pro-Tox-II software. As a case study, we selected artemisinin derivatives to evaluate the platform and to provide a list of safe artemisinin derivatives. Artemisinin from Artemisia annua was described first as an anti-malarial compound and later its anticancer properties were discovered. Here, random forest feature selection algorithm was used for the establishment of cardiotoxicity models. High AUC scores above 0.830 were achieved for all five cardiotoxicity indications. Using a chemical library of 374 artemisinin derivatives as a case study, 7 compounds (deoxydihydro-artemisinin, 3-hydroxy-deoxy-dihydroartemisinin, 3-desoxy-dihydroartemisinin, dihydroartemisinin-furano acetate-d3, deoxyartemisinin, artemisinin G, artemisinin B) passed the toxicity filtering process for hepatotoxicity, mutagenicity, tumorigenicity, and reproductive toxicity in addition to cardiotoxicity. Experimental validation with the cardiomyocyte cell line AC16 supported the findings from the in silico cardiotoxicity model predictions. Transcriptomic profiling of AC16 cells upon artemisinin B treatment revealed a similar gene expression profile as that of the control compound, dexrazoxane. In vivo experiments with a Zebrafish model further substantiated the in silico and in vitro data, as only slight cardiotoxicity in picomolar range was observed. In conclusion, our machine-learning approach combined with in vitro and in vivo experimentation represents a suitable method to predict cardiotoxicity of drug candidates.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany
| | - Sabine M Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | | | - Letian Shan
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128, Mainz, Germany.
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16
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Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Comput Biol Med 2021; 133:104359. [PMID: 33845270 PMCID: PMC8008812 DOI: 10.1016/j.compbiomed.2021.104359] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a major threat worldwide due to its fast spreading. As yet, there are no established drugs available. Speeding up drug discovery is urgently required. We applied a workflow of combined in silico methods (virtual drug screening, molecular docking and supervised machine learning algorithms) to identify novel drug candidates against COVID-19. We constructed chemical libraries consisting of FDA-approved drugs for drug repositioning and of natural compound datasets from literature mining and the ZINC database to select compounds interacting with SARS-CoV-2 target proteins (spike protein, nucleocapsid protein, and 2′-o-ribose methyltransferase). Supported by the supercomputer MOGON, candidate compounds were predicted as presumable SARS-CoV-2 inhibitors. Interestingly, several approved drugs against hepatitis C virus (HCV), another enveloped (−) ssRNA virus (paritaprevir, simeprevir and velpatasvir) as well as drugs against transmissible diseases, against cancer, or other diseases were identified as candidates against SARS-CoV-2. This result is supported by reports that anti-HCV compounds are also active against Middle East Respiratory Virus Syndrome (MERS) coronavirus. The candidate compounds identified by us may help to speed up the drug development against SARS-CoV-2.
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17
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Silva J, Carry E, Xue C, Zhang J, Liang J, Roberge JY, Davies DL. A Novel Dual Drug Approach That Combines Ivermectin and Dihydromyricetin (DHM) to Reduce Alcohol Drinking and Preference in Mice. Molecules 2021; 26:molecules26061791. [PMID: 33810134 PMCID: PMC8004700 DOI: 10.3390/molecules26061791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Alcohol use disorder (AUD) affects over 18 million people in the US. Unfortunately, pharmacotherapies available for AUD have limited clinical success and are under prescribed. Previously, we established that avermectin compounds (ivermectin [IVM] and moxidectin) reduce alcohol (ethanol/EtOH) consumption in mice, but these effects are limited by P-glycoprotein (Pgp/ABCB1) efflux. The current study tested the hypothesis that dihydromyricetin (DHM), a natural product suggested to inhibit Pgp, will enhance IVM potency as measured by changes in EtOH consumption. Using a within-subjects study design and two-bottle choice study, we tested the combination of DHM (10 mg/kg; i.p.) and IVM (0.5–2.5 mg/kg; i.p.) on EtOH intake and preference in male and female C57BL/6J mice. We also conducted molecular modeling studies of DHM with the nucleotide-binding domain of human Pgp that identified key binding residues associated with Pgp inhibition. We found that DHM increased the potency of IVM in reducing EtOH consumption, resulting in significant effects at the 1.0 mg/kg dose. This combination supports our hypothesis that inhibiting Pgp improves the potency of IVM in reducing EtOH consumption. Collectively, we demonstrate the feasibility of this novel combinatorial approach in reducing EtOH consumption and illustrate the utility of DHM in a novel combinatorial approach.
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Affiliation(s)
- Joshua Silva
- Titus Family Department of Clinical Pharmacy, University of Southern California School of Pharmacy, Los Angeles, CA 90089, USA; (J.S.); (C.X.); (J.Z.); (J.L.)
| | - Eileen Carry
- Molecular Design and Synthesis Group, Rutgers University Biomedical Research Innovation Core, Piscataway, NJ 08854, USA; (E.C.); (J.Y.R.)
| | - Chen Xue
- Titus Family Department of Clinical Pharmacy, University of Southern California School of Pharmacy, Los Angeles, CA 90089, USA; (J.S.); (C.X.); (J.Z.); (J.L.)
| | - Jifeng Zhang
- Titus Family Department of Clinical Pharmacy, University of Southern California School of Pharmacy, Los Angeles, CA 90089, USA; (J.S.); (C.X.); (J.Z.); (J.L.)
| | - Jing Liang
- Titus Family Department of Clinical Pharmacy, University of Southern California School of Pharmacy, Los Angeles, CA 90089, USA; (J.S.); (C.X.); (J.Z.); (J.L.)
| | - Jacques Y. Roberge
- Molecular Design and Synthesis Group, Rutgers University Biomedical Research Innovation Core, Piscataway, NJ 08854, USA; (E.C.); (J.Y.R.)
| | - Daryl L. Davies
- Titus Family Department of Clinical Pharmacy, University of Southern California School of Pharmacy, Los Angeles, CA 90089, USA; (J.S.); (C.X.); (J.Z.); (J.L.)
- Correspondence: ; Tel.: +13-23-442-1427
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18
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Esposito C, Wang S, Lange UEW, Oellien F, Riniker S. Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. J Chem Inf Model 2020; 60:4730-4749. [DOI: 10.1021/acs.jcim.0c00525] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carmen Esposito
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Udo E. W. Lange
- Neuroscience Discovery, Medicinal Chemistry, AbbVie Deutschland GmbH & Co KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Frank Oellien
- Neuroscience Discovery, Medicinal Chemistry, AbbVie Deutschland GmbH & Co KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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