1
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Seck I, Ndoye SF, Kapchoup MVK, Nguemo F, Ciss I, Ba LA, Ba A, Sokhna S, Seck M. Effects of plant extracts and derivatives on cardiac K +, Nav, and Ca v channels: a review. Nat Prod Res 2024:1-28. [PMID: 38586947 DOI: 10.1080/14786419.2024.2337112] [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: 11/14/2023] [Accepted: 03/24/2024] [Indexed: 04/09/2024]
Abstract
Natural products (NPs) are endless sources of compounds for fighting against several pathologies. Many dysfunctions, including cardiovascular disorders, such as cardiac arrhythmias have their modes of action regulation of the concentration of electrolytes inside and outside the cell targeting ion channels. Here, we highlight plant extracts and secondary metabolites' effects on the treatment of related cardiac pathologies on hERG, Nav, and Cav of cardiomyocytes. The natural product's pharmacology of expressed receptors like alpha-adrenergic receptors causes an influx of Ca2+ ions through receptor-operated Ca2+ ion channels. We also examine the NPs associated with cardiac contractions such as myocardial contractility by reducing the L-type calcium current and decreasing the intracellular calcium transient, inhibiting the K+ induced contractions, decreasing amplitude of myocyte shortening and showed negative ionotropic and chronotropic effects due to decreasing cytosolic Ca2+. We examine whether the NPs block potassium channels, particular the hERG channel and regulatory effects on Nav1.7.
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Affiliation(s)
- Insa Seck
- Laboratoire de Chimie de Coordination Organique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
- Laboratoire de Chimie Organique et Thérapeutique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Samba Fama Ndoye
- Laboratoire de Chimie Organique et Thérapeutique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | | | - Filomain Nguemo
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Ismaila Ciss
- Laboratoire de Chimie Organique et Thérapeutique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Lalla Aicha Ba
- Laboratoire de Chimie Organique et Thérapeutique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Abda Ba
- Laboratoire de Chimie Organique et Thérapeutique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Seynabou Sokhna
- Laboratoire de Chimie Organique et Thérapeutique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Matar Seck
- Laboratoire de Chimie Organique et Thérapeutique, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
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2
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Wardas B, Schneider JG, Klugbauer N, Flockerzi V, Beck A. Englerin A Inhibits T-Type Voltage-Gated Calcium Channels at Low Micromolar Concentrations. Mol Pharmacol 2023; 104:144-153. [PMID: 37399325 DOI: 10.1124/molpharm.122.000651] [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: 11/28/2022] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 07/05/2023] Open
Abstract
Englerin A (EA) is a potent agonist of tetrameric transient receptor potential canonical (TRPC) ion channels containing TRPC4 and TRPC5 subunits. TRPC proteins form cation channels that are activated by plasma membrane receptors. They convert extracellular signals such as angiotensin II into cellular responses, whereupon Na+ and Ca2+ influx and depolarization of the plasma membrane occur. Via depolarization, voltage-gated Ca2+ (CaV) channels can be activated, further increasing Ca2+ influx. We investigated the extent to which EA also affects the functions of CaV channels using the high-voltage-activated L-type Ca2+ channel CaV1.2 and the low-voltage-activated T-type Ca2+ channels CaV3.1, CaV3.2, and CaV3.3. After expression of cDNAs in human embryonic kidney (HEK293) cells, EA inhibited currents through all T-type channels at half-maximal inhibitory concentrations (IC50) of 7.5 to 10.3 μM. In zona glomerulosa cells of the adrenal gland, angiotensin II-induced elevation of cytoplasmic Ca2+ concentration leads to aldosterone release. We identified transcripts of low- and high-voltage-activated CaV channels and of TRPC1 and TRPC5 in the human adrenocortical (HAC15) zona glomerulosa cell line. Although no EA-induced TRPC activity was measurable, Ca2+ channel blockers distinguished T- and L-type Ca2+ currents. EA blocked 60% of the CaV current in HAC15 cells and T- and L-type channels analyzed at -30 mV and 10 mV were inhibited with IC50 values of 2.3 and 2.6 μM, respectively. Although the T-type blocker Z944 reduced basal and angiotensin II-induced 24-hour aldosterone release, EA was not effective. In summary, we show here that EA blocks CaV1.2 and T-type CaV channels at low-micromolar concentrations. SIGNIFICANCE STATEMENT: In this study we showed that englerin A (EA), a potent agonist of tetrameric transient receptor potential canonical (TRPC)4- or TRPC5-containing channels and currently under investigation to treat certain types of cancer, also inhibits the L-type voltage-gated Ca2+ (CaV) channel CaV1.2 and the T-type CaV channels CaV3.1, CaV3.2, and CaV3.3 channels at low micromolar concentrations.
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Affiliation(s)
- Barbara Wardas
- Experimentelle und Klinische Pharmakologie und Toxikologie/PZMS, Universität des Saarlandes, Homburg, Germany (B.W., V.F., A.B.); Department of Internal Medicine II, Universitätsklinikum des Saarlandes und Medizinische Fakultät der Universität des Saarlandes, Homburg, Germany (J.G.S.); Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg (J.G.S.); and Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany (N.K.)
| | - Jochen G Schneider
- Experimentelle und Klinische Pharmakologie und Toxikologie/PZMS, Universität des Saarlandes, Homburg, Germany (B.W., V.F., A.B.); Department of Internal Medicine II, Universitätsklinikum des Saarlandes und Medizinische Fakultät der Universität des Saarlandes, Homburg, Germany (J.G.S.); Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg (J.G.S.); and Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany (N.K.)
| | - Norbert Klugbauer
- Experimentelle und Klinische Pharmakologie und Toxikologie/PZMS, Universität des Saarlandes, Homburg, Germany (B.W., V.F., A.B.); Department of Internal Medicine II, Universitätsklinikum des Saarlandes und Medizinische Fakultät der Universität des Saarlandes, Homburg, Germany (J.G.S.); Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg (J.G.S.); and Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany (N.K.)
| | - Veit Flockerzi
- Experimentelle und Klinische Pharmakologie und Toxikologie/PZMS, Universität des Saarlandes, Homburg, Germany (B.W., V.F., A.B.); Department of Internal Medicine II, Universitätsklinikum des Saarlandes und Medizinische Fakultät der Universität des Saarlandes, Homburg, Germany (J.G.S.); Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg (J.G.S.); and Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany (N.K.)
| | - Andreas Beck
- Experimentelle und Klinische Pharmakologie und Toxikologie/PZMS, Universität des Saarlandes, Homburg, Germany (B.W., V.F., A.B.); Department of Internal Medicine II, Universitätsklinikum des Saarlandes und Medizinische Fakultät der Universität des Saarlandes, Homburg, Germany (J.G.S.); Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg (J.G.S.); and Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany (N.K.)
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3
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Neo SP, Alli-Shaik A, Wee S, Lim Z, Gunaratne J. Englerin A Rewires Phosphosignaling via Hsp27 Hyperphosphorylation to Induce Cytotoxicity in Renal Cancer Cells. J Proteome Res 2022; 21:1948-1960. [PMID: 35838755 DOI: 10.1021/acs.jproteome.2c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Englerin A (EA) is a small-molecule natural product with selective cytotoxicity against renal cancer cells. EA has been shown to induce apoptosis and cell death through cell-cycle arrest and/or insulin signaling pathways. However, its biological mode of action or targets in renal cancer remains enigmatic. In this study, we employed advanced mass spectrometry-based phosphoproteomics approaches to identify EA's functional roles in renal cancer. We identified 10,940 phosphorylation sites, of which 706 sites exhibited EA-dependent phosphorylation changes. Integrated analysis of motifs and interaction networks suggested activation of stress-activated kinases including p38 upon EA treatment. Of note, a downstream target of p38, Hsp27, was found to be hyperphosphorylated on multiple sites upon EA treatment. Among these, a novel site Ser65 on Hsp27, which was further validated by targeted proteomics, was shown to be crucial for EA-induced cytotoxicity in renal cancer cells. Taken together, these data reveal the complex signaling cascade that is induced upon EA treatment and importantly provide insights into its effects on downstream molecular signaling.
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Affiliation(s)
- Suat Peng Neo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Asfa Alli-Shaik
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Sheena Wee
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Zijie Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore 138673, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore 117597, Singapore
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4
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Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022; 13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.
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Affiliation(s)
- F I Saldívar-González
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - V D Aldas-Bulos
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
| | - J L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - F Plisson
- CONACYT - Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
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5
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Li G, Lin P, Wang K, Gu CC, Kusari S. Artificial intelligence-guided discovery of anticancer lead compounds from plants and associated microorganisms. Trends Cancer 2021; 8:65-80. [PMID: 34750090 DOI: 10.1016/j.trecan.2021.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022]
Abstract
Plants and associated microorganisms are essential sources of natural products against human cancer diseases, partly exemplified by plant-derived anticancer drugs such as Taxol (paclitaxel). Natural products provide diverse mechanisms of action and can be used directly or as prodrugs for further anticancer optimization. Despite the success, major bottlenecks can delay anticancer lead discovery and implementation. Recent advances in sequencing and omics-related technology have provided a mine of information for developing new therapeutics from natural products. Artificial intelligence (AI), including machine learning (ML), has offered powerful techniques for extensive data analysis and prediction-making in anticancer leads discovery. This review presents an overview of current AI-guided solutions to discover anticancer lead compounds, focusing on natural products from plants and associated microorganisms.
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Affiliation(s)
- Gang Li
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao 266071, People's Republic of China.
| | - Ping Lin
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao 266071, People's Republic of China
| | - Ke Wang
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao 266071, People's Republic of China
| | - Chen-Chen Gu
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao 266071, People's Republic of China
| | - Souvik Kusari
- Center for Mass Spectrometry, Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund 44227, Germany.
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6
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Shi C, Yang EJ, Tao S, Ren G, Mou PK, Shim JS. Natural products targeting cancer cell dependency. J Antibiot (Tokyo) 2021; 74:677-686. [PMID: 34163025 DOI: 10.1038/s41429-021-00438-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Precision cancer medicine is a tailored treatment approach for individual cancer patients with different genomic characteristics. Mutated or hyperactive oncogenes have served as main drug targets in current precision cancer medicine, while defective or inactivated tumor suppressors in general have not been considered as druggable targets. Synthetic lethality is one of very few approaches that enable to target defective tumor suppressors with pharmacological agents. Synthetic lethality exploits cancer cell dependency on a protein or pathway, which arises when the function of a tumor suppressor is defective. This approach has been proven to be effective in clinical settings since the successful clinical introduction of BRCA-PARP synthetic lethality for the treatment of breast and ovarian cancer with defective BRCA. Subsequently, large-scale screenings with RNAi, CRISPR/Cas9-sgRNAs, and chemical libraries have been applied to identify synthetic lethal partners of tumor suppressors. Natural products are an important source for the discovery of pharmacologically active small molecules. However, little effort has been made in the discovery of synthetic lethal small molecules from natural products. This review introduces recent advances in the discovery of natural products targeting cancer cell dependency and discusses potentials of natural products in the precision cancer medicine.
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Affiliation(s)
- Changxiang Shi
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Eun Ju Yang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Shishi Tao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Guowen Ren
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Pui Kei Mou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Joong Sup Shim
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China. .,MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR, China.
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7
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Mathai N, Chen Y, Kirchmair J. Validation strategies for target prediction methods. Brief Bioinform 2021; 21:791-802. [PMID: 31220208 PMCID: PMC7299289 DOI: 10.1093/bib/bbz026] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/14/2019] [Accepted: 02/17/2019] [Indexed: 12/11/2022] Open
Abstract
Computational methods for target prediction, based on molecular similarity and network-based approaches, machine learning, docking and others, have evolved as valuable and powerful tools to aid the challenging task of mode of action identification for bioactive small molecules such as drugs and drug-like compounds. Critical to discerning the scope and limitations of a target prediction method is understanding how its performance was evaluated and reported. Ideally, large-scale prospective experiments are conducted to validate the performance of a model; however, this expensive and time-consuming endeavor is often not feasible. Therefore, to estimate the predictive power of a method, statistical validation based on retrospective knowledge is commonly used. There are multiple statistical validation techniques that vary in rigor. In this review we discuss the validation strategies employed, highlighting the usefulness and constraints of the validation schemes and metrics that are employed to measure and describe performance. We address the limitations of measuring only generalized performance, given that the underlying bioactivity and structural data are biased towards certain small-molecule scaffolds and target families, and suggest additional aspects of performance to consider in order to produce more detailed and realistic estimates of predictive power. Finally, we describe the validation strategies that were employed by some of the most thoroughly validated and accessible target prediction methods.
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Affiliation(s)
- Neann Mathai
- Department of Chemistry, University of Bergen, Bergen, Norway.,Computational Biology Unit (CBU), University of Bergen, Bergen, Norway.,Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
| | - Ya Chen
- Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
| | - Johannes Kirchmair
- Department of Chemistry, University of Bergen, Bergen, Norway.,Computational Biology Unit (CBU), University of Bergen, Bergen, Norway.,Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
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8
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Conde J, Pumroy RA, Baker C, Rodrigues T, Guerreiro A, Sousa BB, Marques MC, de Almeida BP, Lee S, Leites EP, Picard D, Samanta A, Vaz SH, Sieglitz F, Langini M, Remke M, Roque R, Weiss T, Weller M, Liu Y, Han S, Corzana F, Morais VA, Faria C, Carvalho T, Filippakopoulos P, Snijder B, Barbosa-Morais NL, Moiseenkova-Bell VY, Bernardes GJL. Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression. ACS CENTRAL SCIENCE 2021; 7:868-881. [PMID: 34079902 PMCID: PMC8161495 DOI: 10.1021/acscentsci.1c00070] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Indexed: 05/04/2023]
Abstract
The use of computational tools to identify biological targets of natural products with anticancer properties and unknown modes of action is gaining momentum. We employed self-organizing maps to deconvolute the phenotypic effects of piperlongumine (PL) and establish a link to modulation of the human transient receptor potential vanilloid 2 (hTRPV2) channel. The structure of the PL-bound full-length rat TRPV2 channel was determined by cryo-EM. PL binds to a transient allosteric pocket responsible for a new mode of anticancer activity against glioblastoma (GBM) in which hTRPV2 is overexpressed. Calcium imaging experiments revealed the importance of Arg539 and Thr522 residues on the antagonistic effect of PL and calcium influx modulation of the TRPV2 channel. Downregulation of hTRPV2 reduces sensitivity to PL and decreases ROS production. Analysis of GBM patient samples associates hTRPV2 overexpression with tumor grade, disease progression, and poor prognosis. Extensive tumor abrogation and long term survival was achieved in two murine models of orthotopic GBM by formulating PL in an implantable scaffold/hydrogel for sustained local therapy. Furthermore, in primary tumor samples derived from GBM patients, we observed a selective reduction of malignant cells in response to PL ex vivo. Our results establish a broadly applicable strategy, leveraging data-motivated research hypotheses for the discovery of novel means tackling cancer.
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Affiliation(s)
- João Conde
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ruth A. Pumroy
- Department
of Systems Pharmacology and Translational Therapeutics, Perelman School
of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Charlotte Baker
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tiago Rodrigues
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Guerreiro
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bárbara B. Sousa
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marta C. Marques
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bernardo P. de Almeida
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sohyon Lee
- Institute
of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Elvira P. Leites
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Daniel Picard
- Department
of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg 69120, Germany
- Department of Pediatric Neuro-Oncogenomics, DKTK, Essen D-45147, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, University Hospital Düsseldorf, Düsseldorf 40225, Germany
| | - Amrita Samanta
- Department
of Systems Pharmacology and Translational Therapeutics, Perelman School
of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sandra H. Vaz
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Florian Sieglitz
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Maike Langini
- Department
of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg 69120, Germany
- Department of Pediatric Neuro-Oncogenomics, DKTK, Essen D-45147, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, University Hospital Düsseldorf, Düsseldorf 40225, Germany
| | - Marc Remke
- Department
of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg 69120, Germany
- Department of Pediatric Neuro-Oncogenomics, DKTK, Essen D-45147, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, University Hospital Düsseldorf, Düsseldorf 40225, Germany
| | - Rafael Roque
- Laboratório
de Neuropatologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHLN) EPE, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tobias Weiss
- Department
of Neurology and Brain Tumour Center, University
Hospital Zürich and University of Zurich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Michael Weller
- Department
of Neurology and Brain Tumour Center, University
Hospital Zürich and University of Zurich, Rämistrasse 100, 8091 Zürich, Switzerland
| | - Yuhang Liu
- Discovery
Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Seungil Han
- Discovery
Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Francisco Corzana
- Departamento
de Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Vanessa A. Morais
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Cláudia
C. Faria
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Department
of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN) EPE, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tânia Carvalho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Panagis Filippakopoulos
- Structural
Genomics Consortium, Oxford University, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Berend Snijder
- Institute
of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Nuno L. Barbosa-Morais
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Vera Y. Moiseenkova-Bell
- Department
of Systems Pharmacology and Translational Therapeutics, Perelman School
of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- E-mail:
| | - Gonçalo J. L. Bernardes
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
- E-mail: ;
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9
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Abstract
Natural products are the most effective source of potential drug leads. The total
synthesis of bioactive natural products plays a crucial role in confirming the hypothetical
complex structure of natural products in the laboratory. The total synthesis of rare bioactive
natural products is one of the great challenges for the organic synthetic community due to
their complex structures, biochemical specificity, and difficult stereochemistry. Subsequently,
the total synthesis is a long process in several cases, and it requires a substantial amount of
time. Microwave irradiation has emerged as a greener tool in organic methodologies to reduce
reaction time from days and hours to minutes and seconds. Moreover, this non-classical
methodology increases product yields and purities, improves reproducibility, modifications of
selectivity, simplification of work-up methods, and reduces unwanted side reactions. Such
beneficial qualities have stimulated this review to cover the application of microwave irradiation in the field of the
total synthesis of bioactive natural products for the first time during the last decade. An overview of the use of microwave
irradiation, natural sources, structures, and biological activities of secondary metabolites is presented elegantly,
focusing on the involvement of at least one or more steps by microwave irradiation as a green technique.
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Affiliation(s)
- Sasadhar Majhi
- Department of Chemistry (UG & PG Department), Triveni Devi Bhalotia College, Raniganj, Kazi Nazrul University, West Bengal- 713347, India
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10
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Chen Y, Kirchmair J. Cheminformatics in Natural Product-based Drug Discovery. Mol Inform 2020; 39:e2000171. [PMID: 32725781 PMCID: PMC7757247 DOI: 10.1002/minf.202000171] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
This review seeks to provide a timely survey of the scope and limitations of cheminformatics methods in natural product-based drug discovery. Following an overview of data resources of chemical, biological and structural information on natural products, we discuss, among other aspects, in silico methods for (i) data curation and natural products dereplication, (ii) analysis, visualization, navigation and comparison of the chemical space, (iii) quantification of natural product-likeness, (iv) prediction of the bioactivities (virtual screening, target prediction), ADME and safety profiles (toxicity) of natural products, (v) natural products-inspired de novo design and (vi) prediction of natural products prone to cause interference with biological assays. Among the many methods discussed are rule-based, similarity-based, shape-based, pharmacophore-based and network-based approaches, docking and machine learning methods.
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Affiliation(s)
- Ya Chen
- Center for Bioinformatics (ZBH)Department of Computer ScienceFaculty of MathematicsInformatics and Natural SciencesUniversität Hamburg20146HamburgGermany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH)Department of Computer ScienceFaculty of MathematicsInformatics and Natural SciencesUniversität Hamburg20146HamburgGermany
- Department of Pharmaceutical ChemistryFaculty of Life SciencesUniversity of Vienna1090ViennaAustria
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11
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Investigation of the Selectivity of L-Type Voltage-Gated Calcium Channels 1.3 for Pyrimidine-2,4,6-Triones Derivatives Based on Molecular Dynamics Simulation. Molecules 2020; 25:molecules25225440. [PMID: 33233858 PMCID: PMC7699898 DOI: 10.3390/molecules25225440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022] Open
Abstract
Human Cav1.3 (hCav1.3) is of great interest as a potential target for Parkinson’s disease. However, common medications like dihydropyridines (DHPs), a kind of classic calcium channel blocker, have poor selectivity to hCav1.3 in clinical treatment, mainly due to being implicated in cardiovascular side-effects mediated by human Cav1.2 (hCav1.2). Recently, pyrimidine-2,4,6-triones (PYTs) have received extensive attention as prominent selective inhibitors to hCav1.3. In this study, we describe the selectivity mechanism of PYTs for hCav1.2 and hCav1.3 based on molecular dynamic simulation methods. Our results reveal that the van der Waals (vdW) interaction was the most important force affecting selectivity. Moreover, the hydrophobic interaction was more conducive to the combination. The highly hydrophobic amino acid residues on hCav1.3, such as V162 (IR1), L303 (IR2), M481 (IR3), and F484 (IR3), provided the greatest contributions in the binding free energy. On the other hand, the substituents of a halogen-substituted aromatic ring, cycloalkyl and norbornyl on PYTs, which are pertinent to the steric hindrance of the compounds, played core roles in the selectivity and affinity for hCav1.3, whereas strong polar substituents needed to be avoided. The findings could provide valuable information for designing more effective and safe medicines for Parkinson’s disease.
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12
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Gonçalo J. L. Bernardes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Gonçalo J. L. Bernardes. Angew Chem Int Ed Engl 2019; 58:17106. [DOI: 10.1002/anie.201906928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Machine learning for target discovery in drug development. Curr Opin Chem Biol 2019; 56:16-22. [PMID: 31734566 DOI: 10.1016/j.cbpa.2019.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]
Abstract
The discovery of macromolecular targets for bioactive agents is currently a bottleneck for the informed design of chemical probes and drug leads. Typically, activity profiling against genetically manipulated cell lines or chemical proteomics is pursued to shed light on their biology and deconvolute drug-target networks. By taking advantage of the ever-growing wealth of publicly available bioactivity data, learning algorithms now provide an attractive means to generate statistically motivated research hypotheses and thereby prioritize biochemical screens. Here, we highlight recent successes in machine intelligence for target identification and discuss challenges and opportunities for drug discovery.
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15
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Tan X, Zhang X, Yu M, Yu Y, Guo Z, Gong T, Niu S, Qin J, Zou Z, Ding G. Sesquiterpenoids and mycotoxin swainsonine from the locoweed endophytic fungus Alternaria oxytropis. PHYTOCHEMISTRY 2019; 164:154-161. [PMID: 31151062 DOI: 10.1016/j.phytochem.2019.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/14/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Oxytropiols A-J, ten undescribed guaiane-type sesquiterpenoids, and the mycotoxin swainsonine (SW) were isolated from the locoweed endophytic fungus Alternaria oxytropis. The chemical structures of these sesquiterpenoids were elucidated on the basis of HR-ESI-MS and NMR data including 1H, 13C, HSQC, 1H-1H COSY, HMBC, and NOESY spectra, and the absolute configurations of these compounds were determined using a modified Mosher's method and X-ray diffraction spectroscopy. A possible biosynthetic pathway of these guaiane-type sesquiterpenoids is discussed, and proposed that post-modification oxidative enzymes might form these highly polyhydroxylated structures. Compound 1 displayed biological effects on the root growth of Arabidopsis thaliana, and SW displayed cytotoxicity against A549 and HeLa cancer cell lines.
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Affiliation(s)
- Xiangmei Tan
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Xiaoyan Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Meng Yu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Yongtao Yu
- School of Agriculture, Ningxia University, Yinchuan, 750021, PR China
| | - Zhe Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Ting Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, PR China
| | - Shubin Niu
- School of Biological Medicine, Beijing City University, Beijing, 450046, PR China
| | - Jianchun Qin
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China
| | - Zhongmei Zou
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China
| | - Gang Ding
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China.
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16
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Guo L, Plietker B. β‐Ketoesters as Mono‐ or Bisnucleophiles: A Concise Enantioselective Total Synthesis of (−)‐Englerin A and B. Angew Chem Int Ed Engl 2019; 58:8346-8350. [DOI: 10.1002/anie.201900401] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/21/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Lei Guo
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Bernd Plietker
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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17
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Rodrigues T, de Almeida BP, Barbosa-Morais NL, Bernardes GJL. Dissecting celastrol with machine learning to unveil dark pharmacology. Chem Commun (Camb) 2019; 55:6369-6372. [PMID: 31089616 DOI: 10.1039/c9cc03116b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
By coalescing bespoke machine learning and bioinformatics analyses with cell-based assays, we unveil the pharmacology of celastrol. Celastrol is a direct modulator of the progesterone and cannabinoid receptors, and its effects correlate with the antiproliferative activity. We demonstrate how in silico methods may drive systems biology studies for natural products.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.
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18
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Guo L, Plietker B. β‐Ketoesters as Mono‐ or Bisnucleophiles: A Concise Enantioselective Total Synthesis of (−)‐Englerin A and B. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Guo
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Bernd Plietker
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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19
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Jeong S, Ko J, Kim M, Park KC, Park EYJ, Kim J, Baik Y, Wie J, Cho AE, Jeon JH, So I. Englerin A-sensing charged residues for transient receptor potential canonical 5 channel activation. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2019; 23:191-201. [PMID: 31080350 PMCID: PMC6488704 DOI: 10.4196/kjpp.2019.23.3.191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 11/17/2022]
Abstract
The transient receptor potential canonical (TRPC) 5 channel, known as a nonselective cation channel, has a crucial role in calcium influx. TRPC5 has been reported to be activated by muscarinic receptor activation and extracellular pH change and inhibited by the protein kinase C pathway. Recent studies have also suggested that TRPC5 is extracellularly activated by englerin A (EA), but the mechanism remains unclear. The purpose of this study is to identify the EA-interaction sites in TRPC5 and thereby clarify the mechanism of TRPC5 activation. TRPC5 channels are over-expressed in human embryonic kidney (HEK293) cells. TRPC5 mutants were generated by site-directed mutagenesis. The whole-cell patch-clamp configuration was used to record TRPC5 currents. Western analysis was also performed to observe the expression of TRPC5 mutants. To identify the EA-interaction site in TRPC5, we first generated pore mutants. When screening the mutants with EA, we observed the EA-induced current increases of TRPC5 abolished in K554N, H594N, and E598Q mutants. The current increases of other mutants were reduced in different levels. We also examined the functional intactness of the mutants that had no effect by EA with TRPC5 agonists, such as carbachol or GTPγS. Our results suggest that the three residues, Lys-554, His-594, and Glu-598, in TRPC5 might be responsible for direct interaction with EA, inducing the channel activation. We also suggest that although other pore residues are not critical, they could partly contribute to the EA-induced channel activation.
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Affiliation(s)
- SeungJoo Jeong
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Juyeon Ko
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Minji Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Ki Chul Park
- Department of Bioinformatics, Korea University, Sejong 30019, Korea
| | - Eunice Yon June Park
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jinsung Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Youngjoo Baik
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jinhong Wie
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Art E Cho
- Department of Bioinformatics, Korea University, Sejong 30019, Korea
| | - Ju-Hong Jeon
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Insuk So
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
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20
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Reker D, Bernardes GJL, Rodrigues T. Computational advances in combating colloidal aggregation in drug discovery. Nat Chem 2019; 11:402-418. [PMID: 30988417 DOI: 10.1038/s41557-019-0234-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
Small molecule effectors are essential for drug discovery. Specific molecular recognition, reversible binding and dose-dependency are usually key requirements to ensure utility of a novel chemical entity. However, artefactual frequent-hitter and assay interference compounds may divert lead optimization and screening programmes towards attrition-prone chemical matter. Colloidal aggregates are the prime source of false positive readouts, either through protein sequestration or protein-scaffold mimicry. Nevertheless, assessment of colloidal aggregation remains somewhat overlooked and under-appreciated. In this Review, we discuss the impact of aggregation in drug discovery by analysing select examples from the literature and publicly-available datasets. We also examine and comment on technologies used to experimentally identify these potentially problematic entities. We focus on evidence-based computational filters and machine learning algorithms that may be swiftly deployed to flag chemical matter and mitigate the impact of aggregates in discovery programmes. We highlight the tools that can be used to scrutinize libraries, and identify and eliminate these problematic compounds.
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Affiliation(s)
- Daniel Reker
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,MIT-IBM Watson AI Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal.
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21
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Baker C, Rodrigues T, de Almeida BP, Barbosa-Morais NL, Bernardes GJL. Natural product-drug conjugates for modulation of TRPV1-expressing tumors. Bioorg Med Chem 2019; 27:2531-2536. [PMID: 30885569 DOI: 10.1016/j.bmc.2019.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/12/2019] [Indexed: 01/22/2023]
Abstract
We report the design, synthesis and biological evaluation of natural product-drug conjugates for treatment of prostate cancers over-expressing the transient receptor potential vanilloid 1 (TRPV1) channel. We validate the relevance of TRPV1 as a target in prostate cancer patients by using a bioinformatics approach and provide proof-of-concept for the drug delivery strategy through bioorthogonal chemistry and stability assays under simulated physiological conditions. In cell-based assays, the constructs displayed modest activity. Moreover, we serendipitously discover that a stoichiometric combination of a TRPV1 agonist with a small, positively charged cytotoxic may provide new research avenues in personalized medicines for prostate cancer.
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Affiliation(s)
- Charlotte Baker
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tiago Rodrigues
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bernardo P de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
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22
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Chen Y, Stork C, Hirte S, Kirchmair J. NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules. Biomolecules 2019; 9:biom9020043. [PMID: 30682850 PMCID: PMC6406893 DOI: 10.3390/biom9020043] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 01/11/2023] Open
Abstract
Natural products (NPs) remain the most prolific resource for the development of small-molecule drugs. Here we report a new machine learning approach that allows the identification of natural products with high accuracy. The method also generates similarity maps, which highlight atoms that contribute significantly to the classification of small molecules as a natural product or synthetic molecule. The method can hence be utilized to (i) identify natural products in large molecular libraries, (ii) quantify the natural product-likeness of small molecules, and (iii) visualize atoms in small molecules that are characteristic of natural products or synthetic molecules. The models are based on random forest classifiers trained on data sets consisting of more than 265,000 to 322,000 natural products and synthetic molecules. Two-dimensional molecular descriptors, MACCS keys and Morgan2 fingerprints were explored. On an independent test set the models reached areas under the receiver operating characteristic curve (AUC) of 0.997 and Matthews correlation coefficients (MCCs) of 0.954 and higher. The method was further tested on data from the Dictionary of Natural Products, ChEMBL and other resources. The best-performing models are accessible as a free web service at http://npscout.zbh.uni-hamburg.de/npscout.
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Affiliation(s)
- Ya Chen
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
| | - Conrad Stork
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
| | - Steffen Hirte
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146 Hamburg, Germany.
- Department of Chemistry, University of Bergen, 5007 Bergen, Norway.
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, 5008 Bergen, Norway.
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23
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A Strength-Weaknesses-Opportunities-Threats (SWOT) Analysis of Cheminformatics in Natural Product Research. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:239-271. [PMID: 31621015 DOI: 10.1007/978-3-030-14632-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cheminformatics-based techniques, such as molecular modeling, docking, virtual screening, and machine learning, are well accepted for their usefulness in drug discovery and development of therapeutically relevant small molecules. Although delayed by several decades, their application in natural product research has led to outstanding findings. Combining information obtained from different sources, i.e., virtual predictions, traditional medicine, structural, biochemical, and biological data, and handling big data effectively will open up new possibilities, but also challenges in the future. Strategies and examples will be presented on how to integrate cheminformatics in pharmacognostic workflows to benefit from these two highly complementary disciplines toward streamlining experimental efforts. While considering their limits and pitfalls and by exploiting their potential, computer-aided strategies should successfully guide future studies and thereby augment our knowledge of bioactive natural lead structures.
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24
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A Toolbox for the Identification of Modes of Action of Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 110 2019; 110:73-97. [DOI: 10.1007/978-3-030-14632-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Abstract
Abstract
The biological pre-validation of natural products (NPs) and their underlying frameworks ensures an unrivaled source of inspiration for chemical probe and drug design. However, the poor knowledge of their drug target counterparts critically hinders the broader exploration of NPs in chemical biology and molecular medicine. Cutting-edge algorithms now provide powerful means for the target deconvolution of phenotypic screen hits and generate motivated research hypotheses. Herein, we present recent progress in artificial intelligence applied to target identification that may accelerate future NP-inspired molecular medicine.
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26
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Rodrigues T, Werner M, Roth J, da Cruz EHG, Marques MC, Akkapeddi P, Lobo SA, Koeberle A, Corzana F, da Silva Júnior EN, Werz O, Bernardes GJL. Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor. Chem Sci 2018; 9:6899-6903. [PMID: 30310622 PMCID: PMC6138237 DOI: 10.1039/c8sc02634c] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/17/2018] [Indexed: 12/04/2022] Open
Abstract
Using machine learning, targets were identified for β-lapachone.
Using machine learning, targets were identified for β-lapachone. Resorting to biochemical assays, β-lapachone was validated as a potent, ligand efficient, allosteric and reversible modulator of 5-lipoxygenase (5-LO). Moreover, we provide a rationale for 5-LO modulation and show that inhibition of 5-LO is relevant for the anticancer activity of β-lapachone. This work demonstrates the power of machine intelligence to deconvolute complex phenotypes, as an alternative and/or complement to chemoproteomics and as a viable general approach for systems pharmacology studies.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Markus Werner
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Jakob Roth
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Eduardo H G da Cruz
- Institute of Exact Sciences , Department of Chemistry , Federal University of Minas Gerais , Belo Horizonte , Brazil
| | - Marta C Marques
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Padma Akkapeddi
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Susana A Lobo
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ;
| | - Andreas Koeberle
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Francisco Corzana
- Departamento de Química , Centro de Investigacíon en Síntesis Química , Universidad de la Rioja , 26006 Logroño , Spain
| | - Eufrânio N da Silva Júnior
- Institute of Exact Sciences , Department of Chemistry , Federal University of Minas Gerais , Belo Horizonte , Brazil
| | - Oliver Werz
- Institute of Pharmacy , Friedrich-Schiller-University Jena , Philosophenweg 14 , D-07743 , Jena , Germany
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular , Faculdade de Medicina da Universidade de Lisboa , Av Prof Egaz Moniz , 1649-028 Lisboa , Portugal . ; .,Department of Chemistry , University of Cambridge , Lensfield Road , CB2 1EW Cambridge , UK .
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27
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Cheung SY, Henrot M, Al-Saad M, Baumann M, Muller H, Unger A, Rubaiy HN, Mathar I, Dinkel K, Nussbaumer P, Klebl B, Freichel M, Rode B, Trainor S, Clapcote SJ, Christmann M, Waldmann H, Abbas SK, Beech DJ, Vasudev NS. TRPC4/TRPC5 channels mediate adverse reaction to the cancer cell cytotoxic agent (-)-Englerin A. Oncotarget 2018; 9:29634-29643. [PMID: 30038709 PMCID: PMC6049859 DOI: 10.18632/oncotarget.25659] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 05/01/2018] [Indexed: 01/09/2023] Open
Abstract
(-)-Englerin A (EA) is a natural product which has potent cytotoxic effects on renal cell carcinoma cells and other types of cancer cell but not non-cancer cells. Although selectively cytotoxic to cancer cells, adverse reaction in mice and rats has been suggested. EA is a remarkably potent activator of ion channels formed by Transient Receptor Potential Canonical 4 and 5 proteins (TRPC4 and TRPC5) and TRPC4 is essential for EA-mediated cancer cell cytotoxicity. Here we specifically investigated the relevance of TRPC4 and TRPC5 to the adverse reaction. Injection of EA (2 mg.kg-1 i.p.) adversely affected mice for about 1 hour, manifesting as a marked reduction in locomotor activity, after which they fully recovered. TRPC4 and TRPC5 single knockout mice were partially protected and double knockout mice fully protected. TRPC4/TRPC5 double knockout mice were also protected against intravenous injection of EA. Importance of TRPC4/TRPC5 channels was further suggested by pre-administration of Compound 31 (Pico145), a potent and selective small-molecule inhibitor of TRPC4/TRPC5 channels which did not cause adverse reaction itself but prevented adverse reaction to EA. EA was detected in the plasma but not the brain and so peripheral mechanisms were implicated but not identified. The data confirm the existence of adverse reaction to EA in mice and suggest that it depends on a combination of TRPC4 and TRPC5 which therefore overlaps partially with TRPC4-dependent cancer cell cytotoxicity. The underlying nature of the observed adverse reaction to EA, as a consequence of TRPC4/TRPC5 channel activation, remains unclear and warrants further investigation.
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Affiliation(s)
- Sin Ying Cheung
- School of Medicine, University of Leeds, Leeds, LS2 9JT, England, UK
| | - Matthias Henrot
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Mohammad Al-Saad
- School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Heiko Muller
- Lead Discovery Center GmbH, D-44227 Dortmund, Germany
| | - Anke Unger
- Lead Discovery Center GmbH, D-44227 Dortmund, Germany
| | - Hussein N Rubaiy
- School of Medicine, University of Leeds, Leeds, LS2 9JT, England, UK
| | - Ilka Mathar
- Institute of Pharmacology, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Klaus Dinkel
- Lead Discovery Center GmbH, D-44227 Dortmund, Germany
| | | | - Bert Klebl
- Lead Discovery Center GmbH, D-44227 Dortmund, Germany
| | - Marc Freichel
- Institute of Pharmacology, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Baptiste Rode
- School of Medicine, University of Leeds, Leeds, LS2 9JT, England, UK
| | - Sebastian Trainor
- School of Medicine, University of Leeds, Leeds, LS2 9JT, England, UK
| | - Steven J Clapcote
- School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Mathias Christmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Herbert Waldmann
- Max-Planck-Institut für Molekulare Physiologie, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, D-44227 Dortmund, Germany
| | - Syed Khawar Abbas
- School of Medicine, University of Leeds, Leeds, LS2 9JT, England, UK
| | - David J Beech
- School of Medicine, University of Leeds, Leeds, LS2 9JT, England, UK
| | - Naveen S Vasudev
- School of Medicine, University of Leeds, Leeds, LS2 9JT, England, UK
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Minard A, Bauer CC, Wright DJ, Rubaiy HN, Muraki K, Beech DJ, Bon RS. Remarkable Progress with Small-Molecule Modulation of TRPC1/4/5 Channels: Implications for Understanding the Channels in Health and Disease. Cells 2018; 7:E52. [PMID: 29865154 PMCID: PMC6025525 DOI: 10.3390/cells7060052] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins of the TRPC family can form many homo- and heterotetrameric cation channels permeable to Na⁺, K⁺ and Ca2+. In this review, we focus on channels formed by the isoforms TRPC1, TRPC4 and TRPC5. We review evidence for the formation of different TRPC1/4/5 tetramers, give an overview of recently developed small-molecule TRPC1/4/5 activators and inhibitors, highlight examples of biological roles of TRPC1/4/5 channels in different tissues and pathologies, and discuss how high-quality chemical probes of TRPC1/4/5 modulators can be used to understand the involvement of TRPC1/4/5 channels in physiological and pathophysiological processes.
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Affiliation(s)
- Aisling Minard
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
| | - Claudia C Bauer
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK.
| | - David J Wright
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK.
| | - Hussein N Rubaiy
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, Hull HU6 7RX, UK.
| | - Katsuhiko Muraki
- Laboratory of Cellular Pharmacology, School of Pharmacy, Aichi-Gakuin University, 1-100 Kusumoto, Chikusa, Nagoya 464-8650, Japan.
| | - David J Beech
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK.
| | - Robin S Bon
- Department of Discovery and Translational Science, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK.
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29
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Rodrigues T. Harnessing the potential of natural products in drug discovery from a cheminformatics vantage point. Org Biomol Chem 2018; 15:9275-9282. [PMID: 29085945 DOI: 10.1039/c7ob02193c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Natural products (NPs) present a privileged source of inspiration for chemical probe and drug design. Despite the biological pre-validation of the underlying molecular architectures and their relevance in drug discovery, the poor accessibility to NPs, complexity of the synthetic routes and scarce knowledge of their macromolecular counterparts in phenotypic screens still hinder their broader exploration. Cheminformatics algorithms now provide a powerful means of circumventing the abovementioned challenges and unlocking the full potential of NPs in a drug discovery context. Herein, I discuss recent advances in the computer-assisted design of NP mimics and how artificial intelligence may accelerate future NP-inspired molecular medicine.
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Affiliation(s)
- Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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30
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Na + entry through heteromeric TRPC4/C1 channels mediates (-)Englerin A-induced cytotoxicity in synovial sarcoma cells. Sci Rep 2017; 7:16988. [PMID: 29209034 PMCID: PMC5717101 DOI: 10.1038/s41598-017-17303-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/22/2017] [Indexed: 12/22/2022] Open
Abstract
The sesquiterpene (-)Englerin A (EA) is an organic compound from the plant Phyllanthus engleri which acts via heteromeric TRPC4/C1 channels to cause cytotoxicity in some types of cancer cell but not normal cells. Here we identified selective cytotoxicity of EA in human synovial sarcoma cells (SW982 cells) and investigated the mechanism. EA induced cation channel current (Icat) in SW982 cells with biophysical characteristics of heteromeric TRPC4/C1 channels. Inhibitors of homomeric TRPC4 channels were weak inhibitors of the Icat and EA-induced cytotoxicity whereas a potent inhibitor of TRPC4/C1 channels (Pico145) strongly inhibited Icat and cytotoxicity. Depletion of TRPC1 converted Icat into a current with biophysical and pharmacological properties of homomeric TRPC4 channels and depletion of TRPC1 or TRPC4 suppressed the cytotoxicity of EA. A Na+/K+-ATPase inhibitor (ouabain) potentiated EA-induced cytotoxicity and direct Na+ loading by gramicidin-A caused Pico145-resistant cytotoxicity in the absence of EA. We conclude that EA has a potent cytotoxic effect on human synovial sarcoma cells which is mediated by heteromeric TRPC4/C1 channels and Na+ loading.
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31
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Wu Z, Zhao S, Fash DM, Li Z, Chain WJ, Beutler JA. Englerins: A Comprehensive Review. JOURNAL OF NATURAL PRODUCTS 2017; 80:771-781. [PMID: 28170253 PMCID: PMC6198806 DOI: 10.1021/acs.jnatprod.6b01167] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the decade since the discovery of englerin A (1) and its potent activity in cancer models, this natural product and its analogues have been the subject of numerous chemical, biological, and preclinical studies by many research groups. This review summarizes published findings and proposes further research directions required for entry of an englerin analogue into clinical trials for kidney cancer and other conditions.
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Affiliation(s)
- Zhenhua Wu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Senzhi Zhao
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - David M. Fash
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Zhenwu Li
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - William J. Chain
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - John A. Beutler
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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32
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Batova A, Altomare D, Creek KE, Naviaux RK, Wang L, Li K, Green E, Williams R, Naviaux JC, Diccianni M, Yu AL. Englerin A induces an acute inflammatory response and reveals lipid metabolism and ER stress as targetable vulnerabilities in renal cell carcinoma. PLoS One 2017; 12:e0172632. [PMID: 28296891 PMCID: PMC5351975 DOI: 10.1371/journal.pone.0172632] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/06/2017] [Indexed: 12/14/2022] Open
Abstract
Renal cell carcinoma (RCC) is among the top ten most common forms of cancer and is the most common malignancy of the kidney. Clear cell renal carcinoma (cc-RCC), the most common type of RCC, is one of the most refractory cancers with an incidence that is on the rise. Screening of plant extracts in search of new anti-cancer agents resulted in the discovery of englerin A, a guaiane sesquiterpene with potent cytotoxicity against renal cancer cells and a small subset of other cancer cells. Though a few cellular targets have been identified for englerin A, it is still not clear what mechanisms account for the cytotoxicity of englerin A in RCC, which occurs at concentrations well below those used to engage the targets previously identified. Unlike any prior study, the current study used a systems biology approach to explore the mechanism(s) of action of englerin A. Metabolomics analyses indicated that englerin A profoundly altered lipid metabolism by 24 h in cc-RCC cell lines and generated significant levels of ceramides that were highly toxic to these cells. Microarray analyses determined that englerin A induced ER stress signaling and an acute inflammatory response, which was confirmed by quantitative PCR and Western Blot analyses. Additionally, fluorescence confocal microscopy revealed that englerin A at 25 nM disrupted the morphology of the ER confirming the deleterious effect of englerin A on the ER. Collectively, our findings suggest that cc-RCC is highly sensitive to disruptions in lipid metabolism and ER stress and that these vulnerabilities can be targeted for the treatment of cc-RCC and possibly other lipid storing cancers. Furthermore, our results suggest that ceramides may be a mediator of some of the actions of englerin A. Lastly, the acute inflammatory response induced by englerin A may mediate anti-tumor immunity.
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Affiliation(s)
- Ayse Batova
- Department of Pediatrics, University of California, San Diego, California, United States of America
- * E-mail:
| | - Diego Altomare
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, United States of America
| | - Kim E. Creek
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, United States of America
| | - Robert K. Naviaux
- Department of Pediatrics, University of California, San Diego, California, United States of America
- The Mitochondrial and Metabolic Disease Center, Department of Pathology, University of California, San Diego, San Diego, California, United States of America
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Lin Wang
- The Mitochondrial and Metabolic Disease Center, Department of Pathology, University of California, San Diego, San Diego, California, United States of America
| | - Kefeng Li
- The Mitochondrial and Metabolic Disease Center, Department of Pathology, University of California, San Diego, San Diego, California, United States of America
| | - Erica Green
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, United States of America
| | - Richard Williams
- Department of Pediatrics, University of California, San Diego, California, United States of America
| | - Jane C. Naviaux
- The Mitochondrial and Metabolic Disease Center, Department of Pathology, University of California, San Diego, San Diego, California, United States of America
| | - Mitchell Diccianni
- Department of Pediatrics, University of California, San Diego, California, United States of America
| | - Alice L. Yu
- Department of Pediatrics, University of California, San Diego, California, United States of America
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
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33
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Nelson R, Gulías M, Mascareñas JL, López F. Concise, Enantioselective, and Versatile Synthesis of (-)-Englerin A Based on a Platinum-Catalyzed [4C+3C] Cycloaddition of Allenedienes. Angew Chem Int Ed Engl 2016; 55:14359-14363. [PMID: 27735111 DOI: 10.1002/anie.201607348] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Indexed: 01/01/2023]
Abstract
A practical synthesis of (-)-englerin A was accomplished in 17 steps and 11 % global yield from commercially available achiral precursors. The key step consists of a platinum-catalyzed [4C+3C] allenediene cycloaddition that directly delivers the trans-fused guaiane skeleton with complete diastereoselectivity. The high enantioselectivity (99 % ee) stems from an asymmetric ruthenium-catalyzed transfer hydrogenation of a readily assembled diene-ynone. The synthesis also features a highly stereoselective oxygenation, and a late-stage cuprate alkylation that enables the preparation of previously inaccessible structural analogues.
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Affiliation(s)
- Ronald Nelson
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Moisés Gulías
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Fernando López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. .,Instituto de Química Orgánica General (CSIC), Juan de la Cierva, 3, 28006, Madrid, Spain.
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34
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Nelson R, Gulías M, Mascareñas JL, López F. Concise, Enantioselective, and Versatile Synthesis of (−)-Englerin A Based on a Platinum-Catalyzed [4C+3C] Cycloaddition of Allenedienes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607348] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ronald Nelson
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Moisés Gulías
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Fernando López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
- Instituto de Química Orgánica General (CSIC); Juan de la Cierva, 3 28006 Madrid Spain
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