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Saoud M, Grau J, Rennert R, Mueller T, Yousefi M, Davari MD, Hause B, Csuk R, Rashan L, Grosse I, Tissier A, Wessjohann LA, Balcke GU. Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404085. [PMID: 39431333 DOI: 10.1002/advs.202404085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/30/2024] [Indexed: 10/22/2024]
Abstract
A bottleneck in the development of new anti-cancer drugs is the recognition of their mode of action (MoA). Metabolomics combined with machine learning allowed to predict MoAs of novel anti-proliferative drug candidates, focusing on human prostate cancer cells (PC-3). As proof of concept, 38 drugs are studied with known effects on 16 key processes of cancer metabolism, profiling low molecular weight intermediates of the central carbon and cellular energy metabolism (CCEM) by LC-MS/MS. These metabolic patterns unveiled distinct MoAs, enabling accurate MoA predictions for novel agents by machine learning. The transferability of MoA predictions based on PC-3 cell treatments is validated with two other cancer cell models, i.e., breast cancer and Ewing's sarcoma, and show that correct MoA predictions for alternative cancer cells are possible, but still at some expense of prediction quality. Furthermore, metabolic profiles of treated cells yield insights into intracellular processes, exemplified for drugs inducing different types of mitochondrial dysfunction. Specifically, it is predicted that pentacyclic triterpenes inhibit oxidative phosphorylation and affect phospholipid biosynthesis, as confirmed by respiration parameters, lipidomics, and molecular docking. Using biochemical insights from individual drug treatments, this approach offers new opportunities, including the optimization of combinatorial drug applications.
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Affiliation(s)
- Mohamad Saoud
- Leibniz Institute of Plant Biochemistry, Dept. of Bioorganic Chemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Jan Grau
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, 06120, Halle (Saale), Germany
| | - Robert Rennert
- Leibniz Institute of Plant Biochemistry, Dept. of Bioorganic Chemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Thomas Mueller
- Martin Luther University Halle-Wittenberg, Medical Faculty, University Clinic for Internal Medicine IV (Hematology/Oncology), 06120, Halle (Saale), Germany
| | - Mohammad Yousefi
- Leibniz Institute of Plant Biochemistry, Dept. of Bioorganic Chemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Mehdi D Davari
- Leibniz Institute of Plant Biochemistry, Dept. of Bioorganic Chemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Bettina Hause
- Leibniz Institute of Plant Biochemistry, Dept. of Cell and Metabolic Biology, Weinberg 3, 06120, Halle (Saale), Germany
| | - René Csuk
- Martin Luther University Halle-Wittenberg, Institute of Chemistry, Department of Organic and Bioorganic Chemistry, 06120, Halle (Saale), Germany
| | - Luay Rashan
- Dhofar University, Research Center, Frankincense Biodiversity Unit, Salalah, 211, Oman
| | - Ivo Grosse
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, 06120, Halle (Saale), Germany
| | - Alain Tissier
- Leibniz Institute of Plant Biochemistry, Dept. of Cell and Metabolic Biology, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ludger A Wessjohann
- Leibniz Institute of Plant Biochemistry, Dept. of Bioorganic Chemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Gerd U Balcke
- Leibniz Institute of Plant Biochemistry, Dept. of Cell and Metabolic Biology, Weinberg 3, 06120, Halle (Saale), Germany
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Albahri G, Badran A, Abdel Baki Z, Alame M, Hijazi A, Daou A, Baydoun E. Potential Anti-Tumorigenic Properties of Diverse Medicinal Plants against the Majority of Common Types of Cancer. Pharmaceuticals (Basel) 2024; 17:574. [PMID: 38794144 PMCID: PMC11124340 DOI: 10.3390/ph17050574] [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: 03/07/2024] [Revised: 04/20/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Globally, cancer is one of the primary causes of both morbidity and mortality. To prevent cancer from getting worse, more targeted and efficient treatment plans must be developed immediately. Recent research has demonstrated the benefits of natural products for several illnesses, and these products have played a significant role in the development of novel treatments whose bioactive components serve as both chemotherapeutic and chemo-preventive agents. Phytochemicals are naturally occurring molecules obtained from plants that have potential applications in both cancer therapy and the development of new medications. These phytochemicals function by regulating the molecular pathways connected to the onset and progression of cancer. Among the specific methods are immune system control, inducing cell cycle arrest and apoptosis, preventing proliferation, raising antioxidant status, and inactivating carcinogens. A thorough literature review was conducted using Google Scholar, PubMed, Scopus, Google Patent, Patent Scope, and US Patent to obtain the data. To provide an overview of the anticancer effects of several medicinal plants, including Annona muricata, Arctium lappa, Arum palaestinum, Cannabis sativa, Catharanthus roseus, Curcuma longa, Glycyrrhiza glabra, Hibiscus, Kalanchoe blossfeldiana, Moringa oleifera, Nerium oleander, Silybum marianum, Taraxacum officinale, Urtica dioica, Withania somnifera L., their availability, classification, active components, pharmacological activities, signaling mechanisms, and potential side effects against the most common cancer types were explored.
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Affiliation(s)
- Ghosoon Albahri
- Plateforme de Recherche et d’Analyse en Sciences de l’Environnement (EDST-PRASE), Beirut P.O. Box 657314, Lebanon; (G.A.); (M.A.); (A.H.)
| | - Adnan Badran
- Department of Nutrition, University of Petra Amman Jordan, Amman P.O. Box 961343, Jordan;
| | - Zaher Abdel Baki
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait;
| | - Mohamad Alame
- Plateforme de Recherche et d’Analyse en Sciences de l’Environnement (EDST-PRASE), Beirut P.O. Box 657314, Lebanon; (G.A.); (M.A.); (A.H.)
| | - Akram Hijazi
- Plateforme de Recherche et d’Analyse en Sciences de l’Environnement (EDST-PRASE), Beirut P.O. Box 657314, Lebanon; (G.A.); (M.A.); (A.H.)
| | - Anis Daou
- Pharmaceutical Sciences Department, College of Pharmacy, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
| | - Elias Baydoun
- Department of Biology, American University of Beirut, Beirut 1107, Lebanon
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Dey P, Tewari N, Dutta S, Newman RA, Chaudhuri TK. Oleander attenuates hepatic inflammation in a TLR4-independent manner and by favorable modulation of hepatocellular global metabolome that supports cytoprotection. JOURNAL OF ETHNOPHARMACOLOGY 2024; 323:117717. [PMID: 38181937 DOI: 10.1016/j.jep.2024.117717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Nerium oleander is used to treat liver-associated chronic metabolic diseases in traditional medicinal systems across the globe. The hepatoprotective effects of oleander are mentioned in Indian and Chinese traditional medicinal literature. AIM OF THE STUDY The present study aimed to investigate the cellular mechanisms behind the hepatoprotective effects of a non-toxic dose of oleander (NO). MATERIALS AND METHODS The hepatoprotective effects of NO were tested against lipopolysaccharide (LPS)-treated HepG2 cells. Oxidative stress response was studied using cellular enzymatic assays, and gene expression was analyzed using qRT-PCR. HepG2 cells were pretreated with TAK-242 (pharmacological inhibitor of TLR4) to decipher the anti-inflammatory mechanisms of NO. Cell-free metabolites were analyzed using GCMS and were subjected to pathway enrichment analysis. RESULTS NO reduced systemic inflammation, serum lipid peroxidation byproducts, and glucose without affecting serum transaminase levels and hepatic histopathological features. NO attenuated the inflammation-induced loss of antioxidant enzyme activities and mRNA expressions of toll-like receptor-4 (TLR4)/nuclear factor κβ (NFκβ)-dependent inflammatory genes. In TAK-242 pretreated cells, LPS was unable to induce inflammatory and oxidative responses. However, NO treatment in TAK-242 pretreated cells with LPS stimulation further reduced the signs of inflammation and improved hepatoprotective activities. A comparative analysis of the intracellular global metabolome from HepG2 cells with and without NO treatment indicated NO-mediated favorable modulation of intracellular metabolic pathways that support cytoprotective activities. CONCLUSION NO protects HepG2 cells from LPS-induced oxidative and inflammatory injury. The hepatoprotective effects of NO are mediated by a TLR4-independent process and through a favorable modulation of the intracellular global metabolome that supports cytoprotection.
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Affiliation(s)
- Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India.
| | - Nisha Tewari
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India.
| | - Somit Dutta
- Department of Development Biology and Genetics, Indian Institute of Science, Bangalore, 560012, India.
| | - Robert A Newman
- University of Texas MD Anderson Cancer Center, Houston, TX, USA; Phoenix Biotechnology, Inc, San Antonio, TX, USA.
| | - Tapas Kumar Chaudhuri
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, India.
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Boulos JC, Chatterjee M, Shan L, Efferth T. In Silico, In Vitro, and In Vivo Investigations on Adapalene as Repurposed Third Generation Retinoid against Multiple Myeloma and Leukemia. Cancers (Basel) 2023; 15:4136. [PMID: 37627164 PMCID: PMC10452460 DOI: 10.3390/cancers15164136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
The majority of hematopoietic cancers in adults are incurable and exhibit unpredictable remitting-relapsing patterns in response to various therapies. The proto-oncogene c-MYC has been associated with tumorigenesis, especially in hematological neoplasms. Therefore, targeting c-MYC is crucial to find effective, novel treatments for blood malignancies. To date, there are no clinically approved c-MYC inhibitors. In this study, we virtually screened 1578 Food and Drug Administration (FDA)-approved drugs from the ZINC15 database against c-MYC. The top 117 compounds from PyRx-based screening with the best binding affinities to c-MYC were subjected to molecular docking studies with AutoDock 4.2.6. Retinoids consist of synthetic and natural vitamin A derivatives. All-trans-retinoic acid (ATRA) were highly effective in hematological malignancies. In this study, adapalene, a third-generation retinoid usually used to treat acne vulgaris, was selected as a potent c-MYC inhibitor as it robustly bound to c-MYC with a lowest binding energy (LBE) of -7.27 kcal/mol, a predicted inhibition constant (pKi) of 4.69 µM, and a dissociation constant (Kd value) of 3.05 µM. Thus, we examined its impact on multiple myeloma (MM) cells in vitro and evaluated its efficiency in vivo using a xenograft tumor zebrafish model. We demonstrated that adapalene exerted substantial cytotoxicity against a panel of nine MM and two leukemic cell lines, with AMO1 cells being the most susceptible one (IC50 = 1.76 ± 0.39 µM) and, hence, the focus of this work. Adapalene (0.5 × IC50, 1 × IC50, 2 × IC50) decreased c-MYC expression and transcriptional activity in AMO1 cells in a dose-dependent manner. An examination of the cell cycle revealed that adapalene halted the cells in the G2/M phase and increased the portion of cells in the sub-G0/G1 phase after 48 and 72 h, indicating that cells failed to initiate mitosis, and consequently, cell death was triggered. Adapalene also increased the number of p-H3(Ser10) positive AMO1 cells, which is a further proof of its ability to prevent mitotic exit. Confocal imaging demonstrated that adapalene destroyed the tubulin network of U2OS cells stably transfected with a cDNA coding for α-tubulin-GFP, refraining the migration of malignant cells. Furthermore, adapalene induced DNA damage in AMO1 cells. It also induced apoptosis and autophagy, as demonstrated by flow cytometry and western blotting. Finally, adapalene impeded tumor growth in a xenograft tumor zebrafish model. In summary, the discovery of the vitamin A derivative adapalene as a c-MYC inhibitor reveals its potential as an avant-garde treatment for MM.
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Affiliation(s)
- Joelle C. Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
| | - Manik Chatterjee
- Translational Oncology, Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany;
| | - Letian Shan
- The First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou 310053, 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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