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Ali S, Shaikh S, Ahmad K, Choi I. Identification of active compounds as novel dipeptidyl peptidase-4 inhibitors through machine learning and structure-based molecular docking simulations. J Biomol Struct Dyn 2023:1-10. [PMID: 38100571 DOI: 10.1080/07391102.2023.2292299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023]
Abstract
The enzyme dipeptidyl peptidase 4 (DPP4) is a potential therapeutic target for type 2 diabetes (T2DM). Many synthetic anti-DPP4 medications are available to treat T2DM. The need for secure and efficient medicines has been unmet due to the adverse side effects of existing DPP4 medications. The present study implemented a combined approach to machine learning and structure-based virtual screening to identify DPP4 inhibitors. Two ML models were trained based on DPP4 IC50 datasets. The ML models random forest (RF) and multilayer perceptron (MLP) neural network showed good accuracy, with the area under the curve being 0.93 and 0.91, respectively. The natural compound library was screened through ML models, and 1% (217) of compounds were selected for further screening. Structure-based virtual screening was performed along with positive control sitagliptin to obtain more specific and selective leads for DPP4. Based on binding affinity, drug-likeness properties, and interaction with DPP4, Z-614 and Z-997 compounds showed high binding affinity and specificity in the catalytic pocket of DPP4. Finally, the stability conformation of the DPP4 enzyme complex was checked by a molecular dynamics (MD) simulation. The MD simulation showed that both compounds bind better in the catalytic pocket, but the Z-614 compound altered the DPP4 native conformation. Therefore, Z-614 showed a high deviation in the backbone. This combined approach (ML and structure-based) study reported that Z-997 binds most stably to DPP4 in their catalytic pocket with a binding free energy of -70.3 kJ/mol, suggesting its therapeutic potential as a treatment option for T2DM disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea
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2
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Oh KK, Choi I, Gupta H, Raja G, Sharma SP, Won SM, Jeong JJ, Lee SB, Cha MG, Kwon GH, Jeong MK, Min BH, Hyun JY, Eom JA, Park HJ, Yoon SJ, Choi MR, Kim DJ, Suk KT. New insight into gut microbiota-derived metabolites to enhance liver regeneration via network pharmacology study. Artif Cells Nanomed Biotechnol 2023; 51:1-12. [PMID: 36562095 DOI: 10.1080/21691401.2022.2155661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We intended to identify favourable metabolite(s) and pharmacological mechanism(s) of gut microbiota (GM) for liver regeneration (LR) through network pharmacology. We utilized the gutMGene database to obtain metabolites of GM, and targets associated with metabolites as well as LR-related targets were identified using public databases. Furthermore, we performed a molecular docking assay on the active metabolite(s) and target(s) to verify the network pharmacological concept. We mined a total of 208 metabolites in the gutMGene database and selected 668 targets from the SEA (1,256 targets) and STP (947 targets) databases. Finally, 13 targets were identified between 61 targets and the gutMGene database (243 targets). Protein-protein interaction network analysis showed that AKT1 is a hub target correlated with 12 additional targets. In this study, we describe the potential microbe from the microbiota (E. coli), chemokine signalling pathway, AKT1 and myricetin that accelerate LR, providing scientific evidence for further clinical trials.
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Affiliation(s)
- Ki-Kwang Oh
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Ickwon Choi
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Haripriya Gupta
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Ganesan Raja
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Satya Priya Sharma
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Sung-Min Won
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Jin-Ju Jeong
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Su-Been Lee
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Min-Gi Cha
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Goo-Hyun Kwon
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Min-Kyo Jeong
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Byeong-Hyun Min
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Ji-Ye Hyun
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Jung-A Eom
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Hee-Jin Park
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Sang-Jun Yoon
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Mi-Ran Choi
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Dong Joon Kim
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
| | - Ki-Tae Suk
- Hallym University College of Medicine, Institute for Liver and Digestive Diseases, Chuncheon, Korea
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González-Castañeda Y, Marrero-Ponce Y, Guerra JO, Echevarría-Díaz Y, Pérez N, Pérez-Giménez F, Simonet AM, Macías FA, Nogueiras CM, Olazabal E, Serrano H. Computational discovery of novel anthelmintic natural compounds from Agave Brittoniana trel. Spp. Brachypus. RB 2022. [DOI: 10.21931/rb/2022.07.04.53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Helminth infections are a medical problem in the world nowadays. This report used bond-based 2D quadratic indices, a bond-level QuBiLs-MAS molecular descriptor family, and Linear Discriminant Analysis (LDA) to obtain a quantitative linear model that discriminates between anthelmintic and non-anthelmintic drug-like organic-compounds. The model obtained correctly classified 87.46% and 81.82% of the training and external data sets, respectively. The developed model was used in a virtual screening to predict the biological activity of all chemicals (19) previously obtained and chemically characterized by some authors of this report from Agave brittoniana Trel. spp. Brachypus. The model identified several metabolites (12) as possible anthelmintics, and a group of 5 novel natural products was tested in an in vitro assay against Fasciola hepatica (100% effectivity at 500 µg/mL). Finally, the two best hits were evaluated in vivo in bald/c mice and the same helminth parasite using a 25 mg/kg dose. Compound 8 (Karatavinoside A) showed an efficacy of 92.2% in vivo. It is important to remark that this natural compound exhibits similar-to-superior activity as triclabendazole, the best human fasciolicide available in the market against Fasciola hepatica, resulting in a novel lead scaffold with anti-helminthic activity.
Keywords: TOMOCOMD-CARDD Software; QuBiLs-MAS, nonstochastic and stochastic bond-based quadratic indices; LDA-based QSAR model; Computational Screening, Anthelmintic Agent; Agave brittoniana Trel. spp. Brachypus, Fasciola hepatica.
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Affiliation(s)
- Yeniel González-Castañeda
- Universidad San Francisco de Quito, Grupo de Medicina Molecular y Traslacional (MeM&T), Escuela de Medicina, Colegio de Ciencias de la Salud (COCSA)
| | - Yovani Marrero-Ponce
- Universidad San Francisco de Quito, Grupo de Medicina Molecular y Traslacional (MeM&T), Escuela de Medicina, Colegio de Ciencias de la Salud (COCSA), Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, Valencia, Spain
| | - Jose O. Guerra
- Chemistry Department, Faculty of Chemistry-Pharmacy. Universidad Central “Marta Abreu” de Las Villas, Santa Clara, 54830, Villa Clara, Cuba
| | - Yunaimy Echevarría-Díaz
- Universidad San Francisco de Quito, Grupo de Medicina Molecular y Traslacional (MeM&T), Escuela de Medicina, Colegio de Ciencias de la Salud (COCSA), Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE)
| | - Noel Pérez
- Colegio de Ciencias e Ingenierías “El Politécnico”, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Facundo Pérez-Giménez
- Unidad de Investigación de Diseño de Fármacos y Conectividad Molecular, Departamento de Química Física, Facultad de Farmacia, Universitat de València, Valencia, Spain
| | - Ana M. Simonet
- Grupo de Alelopatía, Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz
| | - Francisco A. Macías
- Grupo de Alelopatía, Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz
| | - Clara M. Nogueiras
- Departamento de Química Orgánica, Facultad de Química, Universidad de La Habana
| | - Ervelio Olazabal
- Chemical Bioactive Center. Universidad Central “Marta Abreu” de Las Villas, Santa Clara
| | - Hector Serrano
- Chemical Bioactive Center. Universidad Central “Marta Abreu” de Las Villas, Santa Clara
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Bitam S, Hamadache M, Hanini S. 2D-QSAR, docking, molecular dynamics, studies of PF-07321332 analogues to identify alternative inhibitors against 3CL pro enzyme in SARS-CoV disease. J Biomol Struct Dyn 2022:1-10. [PMID: 35983623 DOI: 10.1080/07391102.2022.2113822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Given the results of the Pfizer-developed inhibitor PF-07321332 in the treatment of the SARS-Covid-19 epidemic, we aimed to identify potential alternatives to this compound by utilizing various methods; we developed 2 D-QSAR models to predict the therapeutic activity of 78 analogues of PF-07321332, three statistical learning techniques including (MLP-ANN), (SVR), and (MLR) were exploited. Various validation approaches were applied to the three models developed following the use of five most relevant descriptors. The study of the characteristics of these descriptors proved that the inhibitory activity of PF-07321332 analogues is specifically affected by the structure of the molecule, its polarizability, and by the hydrogen bonds. The best model, named MLP-ANN (with a 5-3-1 architecture), was selected on the basis of the following statistical parameters: r2 = 0.922, Q2 = 0.921. In addition, we performed a molecular docking and a molecular dynamics analysis of these compounds. The obtained results confirm that compound 8 can be a good alternative for compound PF-07321332.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Said Bitam
- Faculté de Technologie, Département du Génie des Procédés et Environnement, Laboratoire des Biomatériaux et Phénomènes de Transport (LBMPT), Université de Médéa, Médéa, Algérie
| | - Mabrouk Hamadache
- Faculté de Technologie, Département du Génie des Procédés et Environnement, Laboratoire des Biomatériaux et Phénomènes de Transport (LBMPT), Université de Médéa, Médéa, Algérie
| | - Salah Hanini
- Faculté de Technologie, Département du Génie des Procédés et Environnement, Laboratoire des Biomatériaux et Phénomènes de Transport (LBMPT), Université de Médéa, Médéa, Algérie
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Lee AG, Kang S, Im S, Pak YK. Cinnamic Acid Attenuates Peripheral and Hypothalamic Inflammation in High-Fat Diet-Induced Obese Mice. Pharmaceutics 2022; 14:pharmaceutics14081675. [PMID: 36015301 PMCID: PMC9413375 DOI: 10.3390/pharmaceutics14081675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Obesity is closely linked to chronic inflammation in peripheral organs and the hypothalamus. Chronic consumption of a high-fat diet (HFD) induces the differentiation of Ly6chigh monocytes into macrophages in adipose tissue, the liver, and the brain, as well as the secretion of pro-inflammatory cytokines. Although cinnamon improves obesity and related diseases, it is unclear which components of cinnamon can affect macrophages and inflammatory cytokines. We performed in silico analyses using ADME, drug-likeness, and molecular docking simulations to predict the active compounds of cinnamon. Among the 82 active compounds of cinnamon, cinnamic acid (CA) showed the highest score of ADME, blood–brain barrier permeability, drug-likeness, and cytokine binding. We then investigated whether CA modulates obesity-induced metabolic profiles and macrophage-related inflammatory responses in HFD-fed mice. While HFD feeding induced obesity, CA ameliorated obesity and related symptoms, such as epididymal fat gain, insulin resistance, glucose intolerance, and dyslipidemia, without hepatic and renal toxicity. CA also improved HFD-induced tumor necrosis factor-α, fat deposition, and macrophage infiltration in the liver and adipose tissue. CA decreased Ly6chigh monocytes, adipose tissue M1 macrophages, and hypothalamic microglial activation. These results suggest that CA attenuates the peripheral and hypothalamic inflammatory monocytes/macrophage system and treats obesity-related metabolic disorders.
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Affiliation(s)
| | - Sora Kang
- Department of Neuroscience, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Suyeol Im
- Department of Neuroscience, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Youngmi Kim Pak
- Department of Neuroscience, Graduate School, Kyung Hee University, Seoul 02447, Korea
- Department of Physiology, College of Medicine, Kyung Hee University, Seoul 02447, Korea
- Correspondence: ; Tel.: +82-2-961-0908
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6
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Yang JR, Chen Q, Wang H, Hu XY, Guo YM, Chen JZ. Reliable CA-(Q)SAR generation based on entropy weight optimized by grid search and correction factors. Comput Biol Med 2022; 146:105573. [DOI: 10.1016/j.compbiomed.2022.105573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/31/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
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7
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da Fonseca AM, Soares NB, Meirú MIL, Colares RP, Neto MM, Sobrinho ACN, Dos Santos HS, Marinho ES. Combined study of docking and molecular dynamics against DNV-3 SN1 protein by bixinoids. J Biomol Struct Dyn 2022:1-11. [PMID: 35510585 DOI: 10.1080/07391102.2022.2070282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Dengue (DENV), Zica virus (ZIKV), and Chikungunya fever (CHIK) are tropical diseases that have caused a lot of problems in general worldwide. Transmitted by mosquitoes of the species Aedes aegypti and albopictus, they have not been completely eradicated in the country, and their proliferation has only increased in the Northeast region. Within the structure of the virus, it is possible to verify the presence of glycoprotein SN1, which is responsible for its replication. If this macromolecule is inhibited using a specific or complex linker, it can interrupt its replication activity. An alternative to this problem has been using structures derived from natural products that have pharmacological properties. A dynamic and molecular docking combined study used computational simulation in the four isomeric forms of bixin against the SN1 protein. The Z,E-bixin and E,E-bixin isomers, both with affinity energy -6.7 and -6.5 Kcal/mol, presented the best results. Thus, bixin and its isomers, found in annatto seeds, maybe an initial proposal in the search for prototype compounds to study to fight this lethal virus in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aluísio Marques da Fonseca
- Institute of Exact Sciences and Nature, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | - Neidelênio Baltazar Soares
- Institute of Exact Sciences and Nature, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | - Maria Imaculada Lourenço Meirú
- Academic Master in Sociobiodiversity and Sustainable Technologies, Institute of Engineering and Sustainable Development, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | - Regilany Paulo Colares
- Institute of Exact Sciences and Nature, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | | | | | | | - Emmanuel Silva Marinho
- Natural Sciences, Science and Technology Center, Ceará State University, Fortaleza, Brazil.,Theoretical and Electrochemical Chemistry Research Group/FAFIDAM, State University of Ceará, Limoeiro do Norte, Brazil
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Cho HM, Zhang M, Park EJ, Lee BW, Park YJ, Kim HW, Pham HTT, Chin YW, Oh WK. Flavonostilbenes Isolated from the Stems of Rhamnoneuron balansae as Potential SIRT1 Activators. J Nat Prod 2022; 85:70-82. [PMID: 35040315 DOI: 10.1021/acs.jnatprod.1c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The cumulative effects of cell damage result in aging, which gradually decreases human function in various aspects and leads to multiple age-related chronic diseases. To overcome the adverse effects of aging, silent mating type information regulation 2 homologue (SIRT1) activators are promising bioactive compounds that mimic calorie restriction to improve quality of life and prevent aging. In this study, 11 new flavonostilbenes (1-11) and three known compounds (12-14) were purified from stems of Rhamnoneuron balansae. The structures of the new compounds were determined using extensive data from spectroscopic methods, including NMR and HRESIMS. Their absolute configurations were deduced by ECD calculations with coupling constant analysis. All of the isolated new compounds (1-11) were evaluated for their effects on SIRT1 deacetylase activity, the NAD+/NADH ratio, and the AMP-activated protein kinase activation level in cell-based assays. The results showed that rhamnoneuronal D (1) exhibits promising biological activity in several in vitro models related to SIRT1 and suggest it is a potential natural-product-based antiaging agent.
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Affiliation(s)
- Hyo-Moon Cho
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Mi Zhang
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun-Jin Park
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ba-Wool Lee
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeon-Joo Park
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun-Woo Kim
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ha-Thanh-Tung Pham
- Department of Botany, Hanoi University of Pharmacy, Hanoi 000084, Vietnam
| | - Young-Won Chin
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Won-Keun Oh
- Korea Bioactive Natural Material Bank, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Najmi A, Javed SA, Al Bratty M, Alhazmi HA. Modern Approaches in the Discovery and Development of Plant-Based Natural Products and Their Analogues as Potential Therapeutic Agents. Molecules 2022; 27:molecules27020349. [PMID: 35056662 PMCID: PMC8779633 DOI: 10.3390/molecules27020349] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022]
Abstract
Natural products represents an important source of new lead compounds in drug discovery research. Several drugs currently used as therapeutic agents have been developed from natural sources; plant sources are specifically important. In the past few decades, pharmaceutical companies demonstrated insignificant attention towards natural product drug discovery, mainly due to its intrinsic complexity. Recently, technological advancements greatly helped to address the challenges and resulted in the revived scientific interest in drug discovery from natural sources. This review provides a comprehensive overview of various approaches used in the selection, authentication, extraction/isolation, biological screening, and analogue development through the application of modern drug-development principles of plant-based natural products. Main focus is given to the bioactivity-guided fractionation approach along with associated challenges and major advancements. A brief outline of historical development in natural product drug discovery and a snapshot of the prominent natural drugs developed in the last few decades are also presented. The researcher’s opinions indicated that an integrated interdisciplinary approach utilizing technological advances is necessary for the successful development of natural products. These involve the application of efficient selection method, well-designed extraction/isolation procedure, advanced structure elucidation techniques, and bioassays with a high-throughput capacity to establish druggability and patentability of phyto-compounds. A number of modern approaches including molecular modeling, virtual screening, natural product library, and database mining are being used for improving natural product drug discovery research. Renewed scientific interest and recent research trends in natural product drug discovery clearly indicated that natural products will play important role in the future development of new therapeutic drugs and it is also anticipated that efficient application of new approaches will further improve the drug discovery campaign.
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Affiliation(s)
- Asim Najmi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia; (A.N.); (M.A.B.); (H.A.A.)
| | - Sadique A. Javed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia; (A.N.); (M.A.B.); (H.A.A.)
- Correspondence:
| | - Mohammed Al Bratty
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia; (A.N.); (M.A.B.); (H.A.A.)
| | - Hassan A. Alhazmi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia; (A.N.); (M.A.B.); (H.A.A.)
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia
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11
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Berlinck RGS, Crnkovic CM, Gubiani JR, Bernardi DI, Ióca LP, Quintana-Bulla JI. The isolation of water-soluble natural products - challenges, strategies and perspectives. Nat Prod Rep 2021; 39:596-669. [PMID: 34647117 DOI: 10.1039/d1np00037c] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Covering period: up to 2019Water-soluble natural products constitute a relevant group of secondary metabolites notably known for presenting potent biological activities. Examples are aminoglycosides, β-lactam antibiotics, saponins of both terrestrial and marine origin, and marine toxins. Although extensively investigated in the past, particularly during the golden age of antibiotics, hydrophilic fractions have been less scrutinized during the last few decades. This review addresses the possible reasons on why water-soluble metabolites are now under investigated and describes approaches and strategies for the isolation of these natural compounds. It presents examples of several classes of hydrosoluble natural products and how they have been isolated. Novel stationary phases and chromatography techniques are also reviewed, providing a perspective towards a renaissance in the investigation of water-soluble natural products.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Camila M Crnkovic
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil
| | - Juliana R Gubiani
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Darlon I Bernardi
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Laura P Ióca
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
| | - Jairo I Quintana-Bulla
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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12
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Taki AC, Byrne JJ, Jabbar A, Lum KY, Hayes S, Addison RS, Ramage KS, Hofmann A, Ekins MG, Wang T, Chang BCH, Davis RA, Gasser RB. High Throughput Screening of the NatureBank 'Marine Collection' in a Haemonchus Bioassay Identifies Anthelmintic Activity in Extracts from a Range of Sponges from Australian Waters. Molecules 2021; 26:5846. [PMID: 34641389 PMCID: PMC8512444 DOI: 10.3390/molecules26195846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/04/2022] Open
Abstract
Widespread resistance in parasitic nematodes to most classes of anthelmintic drugs demands the discovery and development of novel compounds with distinct mechanisms of action to complement strategic or integrated parasite control programs. Products from nature-which assume a diverse 'chemical space'-have significant potential as a source of anthelmintic compounds. In the present study, we screened a collection of extracts (n = 7616) derived from marine invertebrates sampled from Australian waters in a high throughput bioassay for in vitro anti-parasitic activity against the barber's pole worm (Haemonchus contortus)-an economically important parasitic nematode of livestock animals. In this high throughput screen (HTS), we identified 58 active extracts that reduced larval motility by ≥70% (at 90 h), equating to an overall 'hit rate' of ~0.8%. Of these 58 extracts, 16 also inhibited larval development by ≥80% (at 168 h) and/or induced 'non-wild-type' (abnormal) larval phenotypes with reference to 'wild-type' (normal) larvae not exposed to extract (negative controls). Most active extracts (54 of 58) originated from sponges, three from chordates (tunicates) and one from a coral; these extracts represented 37 distinct species/taxa of 23 families. An analysis of samples by 1H NMR fingerprinting was utilised to dereplicate hits and to prioritise a set of 29 sponge samples for future chemical investigation. Overall, these results indicate that a range of sponge species from Australian waters represents a rich source of natural compounds with nematocidal or nematostatic properties. Our plan now is to focus on in-depth chemical investigations of the sample set prioritised herein.
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Affiliation(s)
- Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (A.J.); (A.H.); (T.W.); (B.C.H.C.)
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (A.J.); (A.H.); (T.W.); (B.C.H.C.)
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (A.J.); (A.H.); (T.W.); (B.C.H.C.)
| | - Kah Yean Lum
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.Y.L.); (S.H.); (R.S.A.); (K.S.R.); (M.G.E.); (R.A.D.)
| | - Sasha Hayes
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.Y.L.); (S.H.); (R.S.A.); (K.S.R.); (M.G.E.); (R.A.D.)
| | - Russell S. Addison
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.Y.L.); (S.H.); (R.S.A.); (K.S.R.); (M.G.E.); (R.A.D.)
| | - Kelsey S. Ramage
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.Y.L.); (S.H.); (R.S.A.); (K.S.R.); (M.G.E.); (R.A.D.)
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (A.J.); (A.H.); (T.W.); (B.C.H.C.)
| | - Merrick G. Ekins
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.Y.L.); (S.H.); (R.S.A.); (K.S.R.); (M.G.E.); (R.A.D.)
- Queensland Museum, South Brisbane, QLD 4101, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (A.J.); (A.H.); (T.W.); (B.C.H.C.)
| | - Bill C. H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (A.J.); (A.H.); (T.W.); (B.C.H.C.)
| | - Rohan A. Davis
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.Y.L.); (S.H.); (R.S.A.); (K.S.R.); (M.G.E.); (R.A.D.)
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (A.J.); (A.H.); (T.W.); (B.C.H.C.)
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13
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Liu M, Han J, Feng Y, Guymer G, Forster PI, Quinn RJ. Antimicrobial Benzyltetrahydroisoquinoline-Derived Alkaloids from the Leaves of Doryphora aromatica. J Nat Prod 2021; 84:676-682. [PMID: 33667101 PMCID: PMC8008450 DOI: 10.1021/acs.jnatprod.0c01093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Four new alkaloids, (R)-nomimantharine trifluoroacetate (2), 12-demethylphaeantharine trifluoroacetate (3), nominanthranal trifluoroacetate (4), and the enolic form of 1-hydroxy-6,7-dimethoxy-2-methylisoquinoline trifluoroacetate (5), together with the known dimeric alkaloid phaeantharine trifluoroacetate (1), have been isolated from the extract of the leaves of the rainforest tree Doryphora aromatica (Monimiaceae). The structures of these compounds were elucidated by HRMS and 1D and 2D NMR data. (R)-Nomimantharine trifluoroacetate (2) contains an ether linkage connecting a benzylisoquinoline unit with a tetrahydroisoquinoline, a novel class of dimeric alkaloid. The absolute configuration of (R)-nomimantharine trifluoroacetate (2) was established via electronic circular dichroism data. The compounds isolated were subjected to in vitro antimicrobial assays against a panel of pathogenic microorganisms, including Mycobacterium smegmatis, M. tuberculosis, Escherichia coli, Staphylococcus aureus (SA), and five clinical isolates of oxacillin/methicillin-resistant S. aureus (MRSA). Phaeantharine trifluoroacetate (1) and (R)-nomimantharine trifluoroacetate (2) showed moderate inhibitory activities against Mycobacteria and MRSA strains.
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Affiliation(s)
- Miaomiao Liu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Jianying Han
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Gordon Guymer
- Queensland
Herbarium, Department of Environment and Science, Brisbane
Botanic Gardens, Brisbane, QLD 4066, Australia
| | - Paul I. Forster
- Queensland
Herbarium, Department of Environment and Science, Brisbane
Botanic Gardens, Brisbane, QLD 4066, Australia
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
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14
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Park H, Jeon J, Kim K, Choi S, Hong S. Structure-Based Virtual Screening and De Novo Design of PIM1 Inhibitors with Anticancer Activity from Natural Products. Pharmaceuticals (Basel) 2021; 14:ph14030275. [PMID: 33803840 PMCID: PMC8003278 DOI: 10.3390/ph14030275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND the proviral insertion site of Moloney murine leukemia (PIM) 1 kinase has served as a therapeutic target for various human cancers due to the enhancement of cell proliferation and the inhibition of apoptosis. METHODS to identify effective PIM1 kinase inhibitors, structure-based virtual screening of natural products of plant origin and de novo design were carried out using the protein-ligand binding free energy function improved by introducing an adequate dehydration energy term. RESULTS as a consequence of subsequent enzyme inhibition assays, four classes of PIM1 kinase inhibitors were discovered, with the biochemical potency ranging from low-micromolar to sub-micromolar levels. The results of extensive docking simulations showed that the inhibitory activity stemmed from the formation of multiple hydrogen bonds in combination with hydrophobic interactions in the ATP-binding site. Optimization of the biochemical potency by chemical modifications of the 2-benzylidenebenzofuran-3(2H)-one scaffold led to the discovery of several nanomolar inhibitors with antiproliferative activities against human breast cancer cell lines. CONCLUSIONS these new PIM1 kinase inhibitors are anticipated to serve as a new starting point for the development of anticancer medicine.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology and Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
- Correspondence: (H.P.); (S.H.); Tel.: +82-23-408-3766 (H.P.); +82-42-350-2811 (S.H.)
| | - Jinwon Jeon
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Kewon Kim
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Soyeon Choi
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea; (J.J.); (K.K.); (S.C.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Correspondence: (H.P.); (S.H.); Tel.: +82-23-408-3766 (H.P.); +82-42-350-2811 (S.H.)
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15
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Lénárt J, Gere A, Causon T, Hann S, Dernovics M, Németh O, Hegedűs A, Halász J. LC-MS based metabolic fingerprinting of apricot pistils after self-compatible and self-incompatible pollinations. Plant Mol Biol 2021; 105:435-447. [PMID: 33296063 PMCID: PMC7892686 DOI: 10.1007/s11103-020-01098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE LC-MS based metabolomics approach revealed that putative metabolites other than flavonoids may significantly contribute to the sexual compatibility reactions in Prunus armeniaca. Possible mechanisms on related microtubule-stabilizing effects are provided. Identification of metabolites playing crucial roles in sexual incompatibility reactions in apricot (Prunus armeniaca L.) was the aim of the study. Metabolic fingerprints of self-compatible and self-incompatible apricot pistils were created using liquid chromatography coupled to time-of-flight mass spectrometry followed by untargeted compound search. Multivariate statistical analysis revealed 15 significant differential compounds among the total of 4006 and 1005 aligned metabolites in positive and negative ion modes, respectively. Total explained variance of 89.55% in principal component analysis (PCA) indicated high quality of differential expression analysis. The statistical analysis showed significant differences between genotypes and pollination time as well, which demonstrated high performance of the metabolic fingerprinting and revealed the presence of metabolites with significant influence on the self-incompatibility reactions. Finally, polyketide-based macrolides similar to peloruside A and a hydroxy sphingosine derivative are suggested to be significant differential metabolites in the experiment. These results indicate a strategy of pollen tubes to protect microtubules and avoid growth arrest involved in sexual incompatibility reactions of apricot.
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Affiliation(s)
- József Lénárt
- Department of Applied Chemistry, Faculty of Food Science, Szent István University, Villányi út 29-43, Budapest, 1118, Hungary
- Department of Genetics and Plant Breeding, Faculty of Horticultural Science, Szent István University, Ménesi út 44, Budapest, 1118, Hungary
| | - Attila Gere
- Department of Postharvest Sciences and Sensory Evaluation, Faculty of Food Science, Szent István University, Villányi út 29-43, 1118, Budapest, Hungary
| | - Tim Causon
- Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Mihály Dernovics
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Brunszvik u. 2, Martonvásár, 2462, Hungary
| | - Olga Németh
- Department of Applied Chemistry, Faculty of Food Science, Szent István University, Villányi út 29-43, Budapest, 1118, Hungary
| | - Attila Hegedűs
- Department of Genetics and Plant Breeding, Faculty of Horticultural Science, Szent István University, Ménesi út 44, Budapest, 1118, Hungary
| | - Júlia Halász
- Department of Genetics and Plant Breeding, Faculty of Horticultural Science, Szent István University, Ménesi út 44, Budapest, 1118, Hungary.
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16
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Tayab MA, Chowdhury KAA, Jabed M, Mohammed Tareq S, Kamal ATMM, Islam MN, Uddin AMK, Hossain MA, Emran TB, Simal-Gandara J. Antioxidant-Rich Woodfordia fruticosa Leaf Extract Alleviates Depressive-Like Behaviors and Impede Hyperglycemia. Plants (Basel) 2021; 10:287. [PMID: 33546288 PMCID: PMC7913287 DOI: 10.3390/plants10020287] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 12/19/2022]
Abstract
Dhaiphul (Woodfordia fruticosa) is a frequently demanded plant in South-East Asian regions for its diverse medicinal values. This study was proposed to examine antioxidant, antidiabetic, and antidepressant potentials of methanol extract of W. fruticosa leaves (MEWF) and its derived n-hexane (NHFMEWF) and ethyl acetate (EAFMEWF) fractions through in vitro, in vivo, and computational models. Among test samples, MEWF and EAFMEWF contained the highest phenolic content and showed maximal antioxidant activity in DPPH radical scavenging and ferric reducing power assays. In comparison, NHFMEWF possessed maximum flavonoid content and a significantly potent α-amylase inhibitory profile comparable with positive control acarbose. In animal models of depression (forced swimming and tail suspension test), EAFMEWF and NHFMEWF demonstrated a dose-dependent antidepressant-like effect; explicitly, the depressive-like behaviors significantly declined in EAFMEWF-treated dosing groups in contrast to the control group. In the computational analysis, previously isolated flavonoid compounds from Dhaiphul leaves manifested potent binding affinity against several key therapeutic target proteins of diabetes and depressive disorders including α-amylase, serotonin transporter, dopamine transporter, and neuronal nitric oxide synthase with varying pharmacokinetics and toxicity profiles. This research's outcomes may provide potential dietary supplements for mitigating hyperglycemia, cellular toxicity, and depressive disorder.
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Affiliation(s)
- Mohammed Abu Tayab
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - Kazi Ashfak Ahmed Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - Md. Jabed
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - Syed Mohammed Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - A. T. M. Mostafa Kamal
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - A. M. Kafil Uddin
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - Mohammad Adil Hossain
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.A.T.); (K.A.A.C.); (M.J.); (S.M.T.); (A.T.M.M.K.); (A.M.K.U.); (M.A.H.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo—Ourense Campus, E32004 Ourense, Spain
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17
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Ganesh KAB, Durairaj K, Narasimhan G, Periyathambi K. Computer aided pharmacokinetic profiling and toxicity analysis of naphthalene. Bioinformation 2021; 17:80-85. [PMID: 34393422 PMCID: PMC8340709 DOI: 10.6026/97320630017080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/31/2020] [Accepted: 01/26/2021] [Indexed: 01/02/2023] Open
Abstract
Naphthalene is an aromatic hydrocarbon used as room freshner. Therefore, it is of interest to document the computer aided pharmacokinetic profiling and toxicity analysis data of naphthalene.
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Affiliation(s)
- Ksv Angu Bala Ganesh
- Research Fellow, Department of Anatomy, Sri Ramachandra Medical College and Research Institute, SRIHER-DU, Porur, Chennai-116,Tamil Nadu, India
| | - Kesavi Durairaj
- Professor, Department of Anatomy, Sri Ramachandra Medical College and Research Institute, SRIHER-DU, Porur,Chennai-116, Tamil Nadu, India
| | - Gopinathan Narasimhan
- Assistant Professor, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, SRIHER-DU, Porur,Chennai-116, Tamil Nadu, India
| | - Kalaivani Periyathambi
- Research Scientist, Centre for Toxicology and Developmental Research (CEFTE), SRIHER-DU, Porur,Chennai-116, Tamil Nadu, India
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18
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Herath HMPD, Taki AC, Sleebs BE, Hofmann A, Nguyen N, Preston S, Davis RA, Jabbar A, Gasser RB. Advances in the discovery and development of anthelmintics by harnessing natural product scaffolds. Adv Parasitol 2021; 111:203-251. [PMID: 33482975 DOI: 10.1016/bs.apar.2020.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Widespread resistance to currently-used anthelmintics represents a major obstacle to controlling parasitic nematodes of livestock animals. Given the reliance on anthelmintics in many control regimens, there is a need for the continued discovery and development of new nematocides. Enabling such a focus are: (i) the major chemical diversity of natural products; (ii) the availability of curated, drug-like extract-, fraction- and/or compound-libraries from natural sources; (iii) the utility and practicality of well-established whole-worm bioassays for Haemonchus contortus-an important parasitic nematodes of livestock-to screen natural product libraries; and (iv) the availability of advanced chromatographic (HPLC), spectroscopic (NMR) and spectrometric (MS) techniques for bioassay-guided fractionation and structural elucidation. This context provides a sound basis for the identification and characterisation of anthelmintic candidates from natural sources. This chapter provides a background on the importance and impact of helminth infections/diseases, parasite control and aspects of drug discovery, and reviews recent work focused on (i) screening well-defined compound libraries to establish the methods needed for large-scale screening of natural extract libraries; (ii) discovering plant and marine extracts with nematocidal or nematostatic activity, and purifying bioactive compounds and assessing their potential for further development; and (iii) synthesising analogues of selected purified natural compounds for the identification of possible 'lead' candidates. The chapter describes some lessons learned from this work and proposes future areas of focus for drug discovery. Collectively, the findings from this recent work show potential for selected natural product scaffolds as candidates for future development. Developing such candidates via future chemical optimisation, efficacy and safety evaluations, broad spectrum activity assessments, and target identification represents an exciting prospect and, if successful, could pave the way to subsequent pre-clinical and clinical evaluations.
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Affiliation(s)
- H M P Dilrukshi Herath
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Aya C Taki
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Brad E Sleebs
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Andreas Hofmann
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia; Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Nghi Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah Preston
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia; Faculty of Science and Technology, Federation University, Ballarat, Victoria, Australia
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Abdul Jabbar
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia.
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19
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Borah P, Hazarika S, Deka S, Venugopala KN, Nair AB, Attimarad M, Sreeharsha N, Mailavaram RP. Application of Advanced Technologies in Natural Product Research: A Review with Special Emphasis on ADMET Profiling. Curr Drug Metab 2020; 21:751-767. [PMID: 32664837 DOI: 10.2174/1389200221666200714144911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/12/2020] [Accepted: 06/17/2020] [Indexed: 12/14/2022]
Abstract
The successful conversion of natural products (NPs) into lead compounds and novel pharmacophores has emboldened the researchers to harness the drug discovery process with a lot more enthusiasm. However, forfeit of bioactive NPs resulting from an overabundance of metabolites and their wide dynamic range have created the bottleneck in NP researches. Similarly, the existence of multidimensional challenges, including the evaluation of pharmacokinetics, pharmacodynamics, and safety parameters, has been a concerning issue. Advancement of technology has brought the evolution of traditional natural product researches into the computer-based assessment exhibiting pretentious remarks about their efficiency in drug discovery. The early attention to the quality of the NPs may reduce the attrition rate of drug candidates by parallel assessment of ADMET profiling. This article reviews the status, challenges, opportunities, and integration of advanced technologies in natural product research. Indeed, emphasis will be laid on the current and futuristic direction towards the application of newer technologies in early-stage ADMET profiling of bioactive moieties from the natural sources. It can be expected that combinatorial approaches in ADMET profiling will fortify the natural product-based drug discovery in the near future.
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Affiliation(s)
- Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Sangeeta Hazarika
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh-221005, India
| | - Satyendra Deka
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa-31982, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa-31982, Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa-31982, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa-31982, Saudi Arabia
| | - Raghu P Mailavaram
- Department of Pharmaceutical Chemistry, Shri Vishnu College of Pharmacy, Vishnupur (Affiliated to Andhra University), Bhimavaram, W.G. Dist., Andhra Pradesh, India
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O’Hagan S, Kell DB. Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products. Mar Drugs 2020; 18:E582. [PMID: 33238416 PMCID: PMC7700180 DOI: 10.3390/md18110582] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
It is known that at least some fluorophores can act as 'surrogate' substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the 'natural' substrates of 'orphan' transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly 'drug-like', and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores along with standard fingerprinting methods and the Tanimoto similarity metric. Results: The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug, as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the "quantitative estimate of drug likeness" technique. It is concluded that this set of fluorophores does overlap with a significant part of both the drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities.
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Affiliation(s)
- Steve O’Hagan
- Department of Chemistry, The University of Manchester, Manchester M13 9PT, UK;
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Molecular, Integrative and Systems Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
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21
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Raghavan AR, Yadav VG. Harnessing emerging paradigms in chemical engineering to accelerate the development of pharmaceutical products. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Adhithi R. Raghavan
- Department of Chemical and Biological Engineering & School of Biomedical Engineering The University of British Columbia Vancouver British Columbia Canada
| | - Vikramaditya G. Yadav
- Department of Chemical and Biological Engineering & School of Biomedical Engineering The University of British Columbia Vancouver British Columbia Canada
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22
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Abstract
In December 2019, a COVID-19 epidemic was discovered in Wuhan, China, and since has disseminated around the world impacting human health for millions. Herein, in-silico drug discovery approaches have been utilized to identify potential natural products (NPs) as Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) inhibitors. The MolPort database that contains over 100,000 NPs was screened and filtered using molecular docking techniques. Based on calculated docking scores, the top 5,000 NPs/natural-like products (NLPs) were selected and subjected to molecular dynamics (MD) simulations followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. Combined 50 ns MD simulations and MM-GBSA calculations revealed nine potent NLPs with binding affinities (ΔGbinding) > -48.0 kcal/mol. Interestingly, among the identified NLPs, four bis([1,3]dioxolo)pyran-5-carboxamide derivatives showed ΔGbinding > -56.0 kcal/mol, forming essential short hydrogen bonds with HIS163 and GLY143 amino acids via dioxolane oxygen atoms. Structural and energetic analyses over 50 ns MD simulation demonstrated NLP-Mpro complex stability. Drug-likeness predictions revealed the prospects of the identified NLPs as potential drug candidates. The findings are expected to provide a novel contribution to the field of COVID-19 drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Khlood A A Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Mohamed-Elamir F Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, El-Tahrir St, Dokki, Giza, Egypt
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Prabhavathi H, Dasegowda KR, Renukananda KH, Lingaraju K, Naika HR. Exploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach. J Biomol Struct Dyn 2020; 39:5471-5485. [PMID: 32643536 DOI: 10.1080/07391102.2020.1790424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The proteins encoded by the two major breast cancer genes (BRCA1 and BRCA2), ensure the stability of DNA and prevent uncontrolled cell growth; mutation of these genes is linked to the development of hereditary breast cancers. Exploration of human breast cancer inhibitors plays a vital role in the drug discovery process. In the current work, in silico studies were performed which involves a computational approach for the identification of active phytocompounds from the diverse set of medicinal plant products against the BRCA receptor. The in silico study through pharmacokinetics and pharmacodynamics properties shown promising outcomes for these phytocompounds data set as breast cancer inhibitors. It was observed that the compounds conformed to the Lipinski's rule of five and had good bioavailability. The drug-likeness model score and ADMET profile of the designed ligands also established their potential as a drug candidate. The docking study provided useful insights on potential target-lead interactions and indicated that the newly designed leads had a good binding affinity for BRCA targets. A pharmacophore model was built to explore the scaffolds for BRCA inhibitory activity. An effort is made to screen an inhibitor against BRCA targets by combining the use of ADMET, docking score, and pharmacophore model.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- H Prabhavathi
- Department of Studies & Research in Biotechnology, Tumkur University, Tumakuru, India
| | - K R Dasegowda
- Department of Biotechnology & Genetics, Ramaiah College of Arts, Science and Commerce, Bangalore, India
| | | | - K Lingaraju
- Department of Studies & Research in Biotechnology, Tumkur University, Tumakuru, India
| | - H Raja Naika
- Department of Studies & Research in Biotechnology, Tumkur University, Tumakuru, India
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24
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Lorenzo VP, Scotti L, da Silva Almeida JRG, Scotti MT. Annonaceae Family Alkaloids as Agents Against Leishmaniasis: A Review and Molecular Docking Evaluation. Curr Drug Metab 2020; 21:482-492. [PMID: 32614742 DOI: 10.2174/1389200221666200702124046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
Leishmaniasis is a neglected disease that affects 15 million people worldwide. Existing treatments are associated with limitations, including high costs and toxicity. Several classes of natural substances have been reported to display leishmanicidal activity in the literature. Isoquinoline alkaloids, which are commonly found in the Annonaceae family, represent an important skeleton for the development of anti-leishmaniasis products. This study presents an overview of the potential use of Annonaceae alkaloids to treat leishmaniasis and describes a molecular docking study examining 215 isoquinoline alkaloids. All selected compounds contain a bisbenzyltetrahydroisoquinoline, suggesting the affinity of this skeleton for the target.
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Abstract
Abstract
The discovery of a new drug is a multidisciplinary and very costly task. One of the major steps is the identification of a lead compound, i.e. a compound with a certain degree of potency and that can be chemically modified to improve its activity, metabolic properties, and pharmacokinetics profiles. Terrestrial sources (plants and fungi), microbes and marine organisms are abundant resources for the discovery of new structurally diverse and biologically active compounds. In this chapter, an attempt has been made to quantify the numbers of known published chemical structures (available in chemical databases) from natural sources. Emphasis has been laid on the number of unique compounds, the most abundant compound classes and the distribution of compounds in terrestrial and marine habitats. It was observed, from the recent investigations, that ~500,000 known natural products (NPs) exist in the literature. About 70 % of all NPs come from plants, terpenoids being the most represented compound class (except in bacteria, where amino acids, peptides, and polyketides are the most abundant compound classes). About 2,000 NPs have been co-crystallized in PDB structures.
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26
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Lautié E, Russo O, Ducrot P, Boutin JA. Unraveling Plant Natural Chemical Diversity for Drug Discovery Purposes. Front Pharmacol 2020; 11:397. [PMID: 32317969 PMCID: PMC7154113 DOI: 10.3389/fphar.2020.00397] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
The screening and testing of extracts against a variety of pharmacological targets in order to benefit from the immense natural chemical diversity is a concern in many laboratories worldwide. And several successes have been recorded in finding new actives in natural products, some of which have become new drugs or new sources of inspiration for drugs. But in view of the vast amount of research on the subject, it is surprising that not more drug candidates were found. In our view, it is fundamental to reflect upon the approaches of such drug discovery programs and the technical processes that are used, along with their inherent difficulties and biases. Based on an extensive survey of recent publications, we discuss the origin and the variety of natural chemical diversity as well as the strategies to having the potential to embrace this diversity. It seemed to us that some of the difficulties of the area could be related with the technical approaches that are used, so the present review begins with synthetizing some of the more used discovery strategies, exemplifying some key points, in order to address some of their limitations. It appears that one of the challenges of natural product-based drug discovery programs should be an easier access to renewable sources of plant-derived products. Maximizing the use of the data together with the exploration of chemical diversity while working on reasonable supply of natural product-based entities could be a way to answer this challenge. We suggested alternative ways to access and explore part of this chemical diversity with in vitro cultures. We also reinforced how important it was organizing and making available this worldwide knowledge in an "inventory" of natural products and their sources. And finally, we focused on strategies based on synthetic biology and syntheses that allow reaching industrial scale supply. Approaches based on the opportunities lying in untapped natural plant chemical diversity are also considered.
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Affiliation(s)
- Emmanuelle Lautié
- Centro de Valorização de Compostos Bioativos da Amazônia (CVACBA)-Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Olivier Russo
- Institut de Recherches Internationales SERVIER, Suresnes, France
| | - Pierre Ducrot
- Molecular Modelling Department, 'PEX Biotechnologie, Chimie & Biologie, Institut de Recherches SERVIER, Croissy-sur-Seine, France
| | - Jean A Boutin
- Institut de Recherches Internationales SERVIER, Suresnes, France
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Abstract
Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.
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Affiliation(s)
- Maria Sorokina
- University Friedrich-Schiller, Lessing Strasse 8, 07743, Jena, Germany.
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28
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Miao WG, Tang C, Ye Y, Quinn RJ, Feng Y. Traditional Chinese medicine extraction method by ethanol delivers drug-like molecules. Chin J Nat Med 2020; 17:713-720. [PMID: 31526507 DOI: 10.1016/s1875-5364(19)30086-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 10/26/2022]
Abstract
Traditional Chinese Medicine (TCM) is an important reservoir for bioactive natural products. TCM extraction methods by water decoction and wine tincture are an integral part of TCM and essential for their widely acknowledged efficacy. In this study, we selected 6 common TCMs that are rich in chemistry to investigate whether the TCM extraction methods deliver molecules with drug-like physical chemical properties. Six TCM herbal materials were extracted by water, 95% ethanol, and sequential hexane, dichloromethane and methanol. The extracts were analyzed by HPLC and 1H NMR. Isolation on one of the extracts yielded 32 compounds, their physical chemical properties were analyzed by Instant JChem. Our results showed that ethanol extraction, which mimics TCM wine tincture, delivered compounds with physical chemical properties compliant to Lipinski's rule of 5.
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Affiliation(s)
- William G Miao
- Griffith Institute of Drug Discovery (GRIDD), Griffith University, Queensland 4111, Australia
| | - Chunping Tang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yang Ye
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ronald J Quinn
- Griffith Institute of Drug Discovery (GRIDD), Griffith University, Queensland 4111, Australia.
| | - Yunjiang Feng
- Griffith Institute of Drug Discovery (GRIDD), Griffith University, Queensland 4111, Australia.
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Cabrera-Pardo JR, Fuentealba J, Gavilán J, Cajas D, Becerra J, Napiórkowska M. Exploring the Multi-Target Neuroprotective Chemical Space of Benzofuran Scaffolds: A New Strategy in Drug Development for Alzheimer's Disease. Front Pharmacol 2020; 10:1679. [PMID: 32082168 PMCID: PMC7005051 DOI: 10.3389/fphar.2019.01679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/23/2019] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is an irreversible and progressive neurodegenerative disorder that slowly destroys memory. The precise mechanism of AD is still not entirely understood and remains under discussion; it is believed to be a multifactorial disease in which a number of mechanisms are involved in its pathogenesis. Worldwide, near 37 million people suffer from the effects of AD. As a cause of death for elderly, it is predicted that AD will rank third in the coming years, just behind cancer and heart disease. Unfortunately, AD remains an incurable condition. Despite the devastating problems associated with AD, there are only four FDA approved drugs for palliative treatment of this pathology. Hence, renewed scientific efforts are required not only to uncover more insights into the AD process but also to develop more efficient pharmacological tools against this disease. Due to the complexity and multiple mechanisms at play in the progression of AD, the development of drugs by rational design is extremely difficult. The existing drugs to fight against Alzheimer's have had limited success, mainly due to their ability to modulate only one of the mechanisms involved in AD. As opposed to single-targeted strategies, the identification of small molecules able to affect multiple pathways involved in Alzheimer's is a promising strategy to develop more efficient medicines against this disease. Central to existing efforts to develop pharmaceuticals controlling AD is the discovery of new chemicals displaying strong neuroactivity. Benzofurans are privileged oxygen containing heterocycles that have a strong neuroprotective behavior, inhibiting several of the important events involved in the AD process. In this review, an approach is presented that relies on expanding the neuroprotective chemical space of benzofuran scaffolds by accessing them from Andean-Patagonian fungi and synthetic sources (chemical libraries). The exploration of the neuroprotective chemical space of these scaffolds has the potential to allow the discovery of substitution patterns that display multi-target neuroactivity against multiple events involved in AD. This benzofuran chemical framework will establish a multi-target chemical space that could set the basis for the development of super drugs against AD.
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Affiliation(s)
- Jaime R. Cabrera-Pardo
- Departamento de Química, Facultad de Ciencias, Universidad del Bio-Bio, Concepción, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States
| | - Jorge Fuentealba
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Javiera Gavilán
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Daniel Cajas
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - José Becerra
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Mariola Napiórkowska
- Chair and Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
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Athar M, Sona AN, Bekono BD, Ntie-kang F. Fundamental physical and chemical concepts behind “drug-likeness” and “natural product-likeness”. Physical Sciences Reviews 2019; 4. [DOI: 10.1515/psr-2018-0101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The discovery of a drug is known to be quite cumbersome, both in terms of the microscopic fundamental research behind it and the industrial scale manufacturing process. A major concern in drug discovery is the acceleration of the process and cost reduction. The fact that clinical trials cannot be accelerated, therefore, emphasizes the need to accelerate the strategies for identifying lead compounds at an early stage. We, herein, focus on the definition of what would be regarded as a “drug-like” molecule and a “lead-like” one. In particular, “drug-likeness” is referred to as resemblance to existing drugs, whereas “lead-likeness” is characterized by the similarity with structural and physicochemical properties of a “lead”compound, i.e. a reference compound or a starting point for further drug development. It is now well known that a huge proportion of the drug discovery is inspired or derived from natural products (NPs), which have larger complexity as well as size when compared with synthetic compounds. Therefore, similar definitions of “drug-likeness” and “lead-likeness” cannot be applied for the NP-likeness. Rather, there is the dire need to define and explain NP-likeness in regard to chemical structure. An attempt has been made here to give an overview of the general concepts associated with NP discovery, and to provide the foundational basis for defining a molecule as a “drug”, a “lead” or a “natural compound.”
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Abstract
Abstract
Our previous work was focused on the fundamental physical and chemical concepts behind “drug-likeness” and “natural product (NP)-likeness”. Herein, we discuss further details on the concepts of “drug-likeness”, “lead-likeness” and “NP-likeness”. The discussion will first focus on NPs as drugs, then a discussion of previous studies in which the complexities of the scaffolds and chemical space of naturally occurring compounds have been compared with synthetic, semisynthetic compounds and the Food and Drug Administration-approved drugs. This is followed by guiding principles for designing “drug-like” natural product libraries for lead compound discovery purposes. In addition, we present a tool for measuring “NP-likeness” of compounds and a brief presentation of machine-learning approaches. A binary quantitative structure–activity relationship for classifying drugs from nondrugs and natural compounds from nonnatural ones is also described. While the studies add to the plethora of recently published works on the “drug-likeness” of NPs, it no doubt increases our understanding of the physicochemical properties that make NPs fall within the ranges associated with “drug-like” molecules.
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Devillers J, Devillers H. Toxicity profiling and prioritization of plant-derived antimalarial agents. SAR QSAR Environ Res 2019; 30:801-824. [PMID: 31565973 DOI: 10.1080/1062936x.2019.1665844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Human malaria is the most widespread mosquito-borne life-threatening disease worldwide. In the absence of effective vaccines, prevention and treatment of malaria only depend on prophylaxis and drug-based therapy either in monotherapy or in combination. Unfortunately, the number of available antimalarial drugs presenting different mechanisms of action is rather limited. In addition, the appearance of drug-resistance in the parasite strains impacts the efficacy of the treatments. As a result, there is a crucial need to find new drugs to circumvent resistance problems. In the quest to identify new antimalarial agents a huge number of plant-derived compounds (PDCs) have been investigated. Surprisingly in the in silico PDC screening programs, toxicity filters are either never used or so simple that their interest is limited. In this context, the goal of this study was to show how to take advantage of validated toxicity QSAR models for refining the selection of PDCs. From an original data set of 507 PDCs collected from the literature, the use of toxicity filters for endocrine disruption, developmental toxicity, and hepatotoxicity in conjunction with classical pharmacokinetic filters allowed us to obtain a list of 31 compounds of potential interest. The pros and cons of such a strategy have been discussed.
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Affiliation(s)
| | - H Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
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Kashyap D, Tuli HS, Yerer MB, Sharma A, Sak K, Srivastava S, Pandey A, Garg VK, Sethi G, Bishayee A. Natural product-based nanoformulations for cancer therapy: Opportunities and challenges. Semin Cancer Biol 2019; 69:5-23. [PMID: 31421264 DOI: 10.1016/j.semcancer.2019.08.014] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/09/2023]
Abstract
Application of natural product-based nanoformulations for the treatment of different human diseases, such as cancer, is an emerging field. The conventional cancer therapeutic modalities, including surgery, chemotherapy, immunotherapy, radiotherapy has limited achievements. A larger number of drawbacks are associated with these therapies, including damage to proliferating healthy tissues, structural deformities, systemic toxicity, long-term side effects, resistance to the drug by tumor cells, and psychological problems. The advent of nanotechnology in cancer therapeutics is recent; however, it has progressed and transformed the field of cancer treatment at a rapid rate. Nanotherapeutics have promisingly overcome the limitations of conventional drug delivery system, i.e., low aqueous solubility, low bioavailability, multidrug resistance, and non-specificity. Specifically, natural product-based nanoformulations are being intentionally studied in different model systems. Where it is found that these nanoformulations has more proximity and reduced side effects. The nanoparticles can specifically target tumor cells, enhancing the specificity and efficacy of cancer therapeutic modalities which in turn improves patient response and survival. The integration of phytotherapy and nanotechnology in the clinical setting may improve pharmacological response and better clinical outcome of patients.
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Affiliation(s)
- Dharambir Kashyap
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh - 160 012, Punjab, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala - 133 207, Haryana, India.
| | - Mukerrem Betul Yerer
- Department of Pharmacology, Faculty of Pharmacy, University of Erciyes, Kayseri 38039, Turkey
| | - Ajay Sharma
- Department of Chemistry, Career Point University, Tikker-Kharwarian, Hamirpur - 176 041, Himachal Pradesh, India
| | | | - Saumya Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad - 211 004, Uttar Pradesh, India
| | - Anjana Pandey
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad - 211 004, Uttar Pradesh, India
| | - Vivek Kumar Garg
- Department of Biochemistry, Government Medical College and Hospital, Sector 32, Chandigarh - 160 031, Punjab, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore.
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA.
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Rodriguez KX, Howe EN, Bacher EP, Burnette M, Meloche JL, Meisel J, Schnepp P, Tan X, Chang M, Zartman J, Zhang S, Ashfeld BL. Combined Scaffold Evaluation and Systems-Level Transcriptome-Based Analysis for Accelerated Lead Optimization Reveals Ribosomal Targeting Spirooxindole Cyclopropanes. ChemMedChem 2019; 14:1653-1661. [PMID: 31140738 DOI: 10.1002/cmdc.201900266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Indexed: 12/22/2022]
Abstract
With evolutionary drug resistance impacting efforts to treat disease, the need for small molecules that exhibit novel molecular mechanisms of action is paramount. In this study, we combined scaffold-directed synthesis with a hybrid experimental and transcriptome analysis to identify bis-spirooxindole cyclopropanes that inhibit cancer cell proliferation through disruption of ribosomal function. These findings demonstrate the value of an integrated, biologically inspired synthesis and assay strategy for the accelerated identification of first-in-class cancer therapeutic candidates.
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Affiliation(s)
- Kevin X Rodriguez
- Department of Chemistry and Biochemistry, University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Erin N Howe
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN, 46556, USA
| | - Emily P Bacher
- Department of Chemistry and Biochemistry, University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Miranda Burnette
- Department of Chemical and Biological Engineering, University of Notre Dame, 182 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
| | - Jennifer L Meloche
- Department of Chemistry and Biochemistry, University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Jayda Meisel
- Department of Chemistry and Biochemistry, University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Patricia Schnepp
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN, 46556, USA
| | - Xuejuan Tan
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN, 46556, USA
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA
| | - Jeremiah Zartman
- Department of Chemical and Biological Engineering, University of Notre Dame, 182 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
| | - Siyuan Zhang
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN, 46556, USA
| | - Brandon L Ashfeld
- Department of Chemistry and Biochemistry, University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA
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Jia X, Li P, Liu X, Lin J, Chu Y, Yu J, Wang J, Liu H, Zhao F. Green and Facile Assembly of Diverse Fused N-Heterocycles Using Gold-Catalyzed Cascade Reactions in Water. Molecules 2019; 24:E988. [PMID: 30862100 DOI: 10.3390/molecules24050988] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/30/2022] Open
Abstract
The present study describes an AuPPh3Cl/AgSbF6-catalyzed cascade reaction between amine nucleophiles and alkynoic acids in water. This process proceeds in high step economy with water as the sole coproduct, and leads to the generation of two rings, together with the formation of three new bonds in a single operation. This green cascade process exhibits valuable features such as low catalyst loading, good to excellent yields, high efficiency in bond formation, excellent selectivity, great tolerance of functional groups, and extraordinarily broad substrate scope. In addition, this is the first example of the generation of an indole/thiophene/pyrrole/pyridine/naphthalene/benzene-fused N-heterocycle library through gold catalysis in water from readily available materials. Notably, the discovery of antibacterial molecules from this library demonstrates its high quality and potential for the identification of active pharmaceutical ingredients.
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Daniyan MO, Ojo OT. In silico identification and evaluation of potential interaction of Azadirachta indica phytochemicals with Plasmodium falciparum heat shock protein 90. J Mol Graph Model 2019; 87:144-164. [DOI: 10.1016/j.jmgm.2018.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/31/2018] [Accepted: 11/30/2018] [Indexed: 01/13/2023]
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Klein-Júnior LC, Corrêa R, Vander Heyden Y, Cechinel Filho V. All that glitters is not gold: Panning cytotoxic natural products and derivatives with a fused tricyclic backbone by the estimation of their leadlikeness for cancer treatment. Eur J Med Chem 2019; 166:1-10. [PMID: 30684866 DOI: 10.1016/j.ejmech.2019.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/12/2019] [Accepted: 01/13/2019] [Indexed: 11/26/2022]
Abstract
Tricyclic compounds call the attention because of their pharmacological properties, and are considered a preferred platform for the development of drugs. Especially, in cancer treatment, these planar compounds are known for their ability to stack with DNA base pairs, acting as intercalators. In this sense, natural products (NPs) are a prodigal source of polycyclic compounds, comprising classes, such as carbolines, anthraquinones and xanthones. However, most of these compounds lack suitable physico-chemical properties, compatible to oral bioaviability. In this perspective, this paper aims to overview the role of tricyclic cores in the development of cytotoxic compounds, focusing on the leadlikeness estimation of the most prominent NP classes and their synthetic derivatives.
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Affiliation(s)
- Luiz Carlos Klein-Júnior
- Chemical-Pharmaceutical Investigation Center, University do Vale do Itajaí - UNIVALI, Rua Uruguai 456, 88.302-202, Itajaí, SC, Brazil.
| | - Rogério Corrêa
- Chemical-Pharmaceutical Investigation Center, University do Vale do Itajaí - UNIVALI, Rua Uruguai 456, 88.302-202, Itajaí, SC, Brazil
| | - Yvan Vander Heyden
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling, Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel - VUB, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Valdir Cechinel Filho
- Chemical-Pharmaceutical Investigation Center, University do Vale do Itajaí - UNIVALI, Rua Uruguai 456, 88.302-202, Itajaí, SC, Brazil
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McAlpine JB, Chen SN, Kutateladze A, MacMillan JB, Appendino G, Barison A, Beniddir MA, Biavatti MW, Bluml S, Boufridi A, Butler MS, Capon RJ, Choi YH, Coppage D, Crews P, Crimmins MT, Csete M, Dewapriya P, Egan JM, Garson MJ, Genta-Jouve G, Gerwick WH, Gross H, Harper MK, Hermanto P, Hook JM, Hunter L, Jeannerat D, Ji NY, Johnson TA, Kingston DGI, Koshino H, Lee HW, Lewin G, Li J, Linington RG, Liu M, McPhail KL, Molinski TF, Moore BS, Nam JW, Neupane RP, Niemitz M, Nuzillard JM, Oberlies NH, Ocampos FMM, Pan G, Quinn RJ, Reddy DS, Renault JH, Rivera-Chávez J, Robien W, Saunders CM, Schmidt TJ, Seger C, Shen B, Steinbeck C, Stuppner H, Sturm S, Taglialatela-Scafati O, Tantillo DJ, Verpoorte R, Wang BG, Williams CM, Williams PG, Wist J, Yue JM, Zhang C, Xu Z, Simmler C, Lankin DC, Bisson J, Pauli GF. The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. Nat Prod Rep 2019; 36:35-107. [PMID: 30003207 PMCID: PMC6350634 DOI: 10.1039/c7np00064b] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 12/20/2022]
Abstract
Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.
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Affiliation(s)
- James B McAlpine
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Shao-Nong Chen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Andrei Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - John B MacMillan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Giovanni Appendino
- Dipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, Universita` del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | | | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Maique W Biavatti
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Stefan Bluml
- University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Young H Choi
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - David Coppage
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Michael T Crimmins
- Kenan and Caudill Laboratories of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marie Csete
- University of Southern California, Huntington Medical Research Institutes, 99 N. El Molino Ave., Pasadena, CA 91101, USA
| | - Pradeep Dewapriya
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Joseph M Egan
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Mary J Garson
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Grégory Genta-Jouve
- C-TAC, UMR 8638 CNRS, Faculté de Pharmacie de Paris, Paris-Descartes University, Sorbonne, Paris Cité, 4, Aveue de l'Observatoire, 75006 Paris, France
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, Eberhard Karls University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Precilia Hermanto
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - James M Hook
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luke Hunter
- NMR Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Damien Jeannerat
- University of Geneva, Department of Organic Chemistry, 30 quai E. Ansermet, CH 1211 Geneva 4, Switzerland
| | - Nai-Yun Ji
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China
| | - Tyler A Johnson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - David G I Kingston
- Department of Chemistry, M/C 0212, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Hiroyuki Koshino
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Guy Lewin
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Tadeusz F Molinski
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA 92093, USA and Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joo-Won Nam
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ram P Neupane
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Matthias Niemitz
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jean-Marc Nuzillard
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Nicholas H Oberlies
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | | | - Guohui Pan
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Jean-Hugues Renault
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - José Rivera-Chávez
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Wolfgang Robien
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Carla M Saunders
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Thomas J Schmidt
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Seger
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Ben Shen
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Christoph Steinbeck
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Hermann Stuppner
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Sonja Sturm
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Orazio Taglialatela-Scafati
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Dean J Tantillo
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Robert Verpoorte
- Division of Pharmacognosy, Section Metabolomics, Institute of Biology, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bin-Gui Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Chunhui Road 17, Yantai 264003, People's Republic of China and Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Craig M Williams
- School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Philip G Williams
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Julien Wist
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Jian-Min Yue
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Chen Zhang
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Zhengren Xu
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. , and
| | - Charlotte Simmler
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - David C Lankin
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Jonathan Bisson
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
| | - Guido F Pauli
- Center for Natural Product Technologies (CENAPT), Program for Collaborative Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. ,
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Abstract
The continued spread of antimicrobial resistance represents one of the most serious infectious disease threats to global health. There is consensus that a key component of addressing this threat is to replenish the waning pipeline of antimicrobials, with attention being paid to novel mechanisms of action. This includes the development of new classes of classic bacteriostatic and bactericidal antibiotics as well as antivirulence drugs, and it is especially in these areas where plant natural products demonstrate great potential. To this end, we discuss the unique characteristics of plant natural products, the advantages of plants as a resource for anti-infective drug discovery, and recent technologies that have further enabled this path of inquiry. As a result of emerging realization of their advantages, plant natural products have recently enjoyed increased scrutiny in antimicrobial lead discovery, and they will continue to serve as a source of leads. We conclude that plant natural products represent a promising and largely untapped source of new chemical entities from which novel anti-infectives can be discovered.
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Affiliation(s)
- Akram M Salam
- Molecular and Systems Pharmacology Program, Laney Graduate School, Emory University, Atlanta, GA, United States
| | - Cassandra L Quave
- Center for the Study of Human Health, Emory University College of Arts and Sciences, Atlanta, GA, United States; Department of Dermatology, Emory University School of Medicine, Atlanta, GA, United States; Antibiotic Resistance Center, Emory University, Atlanta, GA, United States; Emory University Herbarium, Atlanta, GA, United States.
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40
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Chibli LA, Schmidt TJ, Nonato MC, Calil FA, Da Costa FB. Natural products as inhibitors of Leishmania major dihydroorotate dehydrogenase. Eur J Med Chem 2018; 157:852-866. [PMID: 30145372 DOI: 10.1016/j.ejmech.2018.08.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/09/2018] [Accepted: 08/11/2018] [Indexed: 12/19/2022]
Abstract
The flavoenzyme dihydroorotate dehydrogenase (DHODH) catalyzes the fourth reaction of the de novo pyrimidine biosynthetic pathway, which exerts vital functions in the cells, especially within DNA and RNA biosynthesis. Thus, this enzyme stands out as a new key molecular target for parasites causing Neglected Diseases (NDs). Focused on contributing to the development of new therapeutic alternatives for NDs, in this study, for the first time, a screening of 57 natural products for in vitro inhibition of Leishmania major DHODH (LmDHODH) was carried out, including cross validation against the human DHODH (HsDHODH). A subset of natural products consisting of 21 sesquiterpene lactones (STLs) was submitted to QSAR studies. Additionally, thermostability studies by differential scanning fluorimetry (DSF) were performed to determine whether the STLs are effectively or not binding to the enzyme. The IC50 values against LmDHODH varied from 27 to 1200 μM; only irrelevant inhibition was obtained on HsDHODH. DSF assays confirmed binding of STLs to LmDHODH; moreover, it is suggested that such inhibitors might act in a different site other than the active site. A reliable QSAR model based on molecular descriptors was obtained (R2: 0.83; Q2CV: 0.69 and Q2EXT/F2: 0.66) indicating that stronger inhibition requires a balanced distribution of the hydrophobic regions across the molecular surface, as well as higher width and lower hydrophobicity of the molecules. A pharmacophore-based 3D-QSAR approach also afforded a useful model (R2: 0.72; Q2CV: 0.50 and Q2EXT/F2: 0.62), which confirmed the importance of proper orientation of the ligands, molecular surface features and shape for stronger inhibition, reflecting properties of a putative common binding site. These data indicated for the first time that natural products can actually inhibit LmDHODH and highlighted some metabolites as potentially interesting starting points for the discovery of more potent LmDHODH inhibitors, ultimately aiming at new effective therapeutic alternatives for leishmaniasis and, possibly, other NDs caused by trypanosomatids.
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Affiliation(s)
- Lucas A Chibli
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903 Ribeirão Preto, SP, Brazil.
| | - Thomas J Schmidt
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Münster, PharmaCampus, Corrensstraße 48, Münster D-48149, Germany.
| | - M Cristina Nonato
- Laboratory of Protein Crystallography, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903 Ribeirão Preto, SP, Brazil.
| | - Felipe A Calil
- Laboratory of Protein Crystallography, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903 Ribeirão Preto, SP, Brazil.
| | - Fernando B Da Costa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, 14040-903 Ribeirão Preto, SP, Brazil.
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Warner CJA, Salinas M, Zamorano-Sánchez D, Bray WM, Lokey RS, Yildiz FH, Linington RG. The Bioactive Lipid (S)-Sebastenoic Acid Impacts Motility and Dispersion in Vibrio cholerae. CAN J CHEM 2018; 96:196-203. [PMID: 34158674 DOI: 10.1139/cjc-2017-0334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although Gram-negative bacterial pathogens continue to impart a substantial burden on global healthcare systems, much remains to be understood about aspects of basic physiology in these organisms. In recent years, cyclic-diguanylate (c-di-GMP) has emerged as a key regulator of a number of important processes related to pathogenicity, including biofilm formation, motility and virulence. In an effort to discover chemical genetic probes for studying V. cholerae we have developed a new motility-based high-throughput screen to identify compounds that modulate c-di-GMP levels. Using this new screening platform, we tested a library of microbially-derived marine natural products extracts, leading to the discovery of the bioactive lipid (S)-sebastenoic acid. Evaluation of the effect of this new compound on bacterial motility, vpsL expression and biofilm formation implied that (S)-sebastenoic acid may alter phenotypes associated to c-di-GMP signaling in V. cholerae.
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Affiliation(s)
- Christopher J A Warner
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mauro Salinas
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Zamorano-Sánchez
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Walter M Bray
- Chemical Screening Center, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Chemical Screening Center, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Roger G Linington
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.,Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, Canada
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42
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O'Hagan S, Kell DB. Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries. Biotechnol J 2017; 13. [PMID: 29168302 DOI: 10.1002/biot.201700503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/09/2017] [Indexed: 01/01/2023]
Abstract
Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates.
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Affiliation(s)
- Steve O'Hagan
- Dr. S. O'Hagan, Prof. D. B. Kell, School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Dr. S. O'Hagan, Prof. D. B. Kell, The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B Kell
- Dr. S. O'Hagan, Prof. D. B. Kell, School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Dr. S. O'Hagan, Prof. D. B. Kell, The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Prof. D. B. Kell, Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
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Abstract
Natural products (NPs) have been used as traditional medicines since antiquity. With more than 1060 estimated compounds with molecular weights less than 500 Da representing chemical space, NPs occupy a very small percentage; however, they are significantly overrepresented in biologically relevant chemical space. The classical approach concentrates on identifying one or more NPs with biological activity from a source organism. There is much more to be learned from NPs than we can discover this narrow view. In this review, we discuss ways to harness the global properties of NPs.
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Affiliation(s)
- Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
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44
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Kim D, Park JY, Kim JH. Docking-based In SilicoScreening for Identification of Micromolar Inhibitors of Tropomyosin-related Kinase A from Natural Origin. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Daehyun Kim
- Department of Chemistry; Chung-Ang University; Seoul 06974 Korea
| | - Jung Youl Park
- Industry-Academic Cooperation Foundation; Hanbat National University; Daejeon 34158 Korea
| | - Ji-Hyun Kim
- National CRI-Center for Chemical Dynamics in Living Cells; Chung-Ang University; Seoul 06974 Korea
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45
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Ibezim A, Debnath B, Ntie-kang F, Mbah CJ, Nwodo NJ. Binding of anti-Trypanosoma natural products from African flora against selected drug targets: a docking study. Med Chem Res 2017; 26:562-79. [DOI: 10.1007/s00044-016-1764-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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46
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Choi H, Cho SY, Pak HJ, Kim Y, Choi JY, Lee YJ, Gong BH, Kang YS, Han T, Choi G, Cho Y, Lee S, Ryoo D, Park H. NPCARE: database of natural products and fractional extracts for cancer regulation. J Cheminform 2017; 9:2. [PMID: 28184254 PMCID: PMC5267755 DOI: 10.1186/s13321-016-0188-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/28/2016] [Indexed: 01/15/2023] Open
Abstract
Background
Natural products have increasingly attracted much attention as a valuable resource for the development of anticancer medicines due to the structural novelty and good bioavailability. This necessitates a comprehensive database for the natural products and the fractional extracts whose anticancer activities have been verified. Description NPCARE (http://silver.sejong.ac.kr/npcare) is a publicly accessible online database of natural products and fractional extracts for cancer regulation. At NPCARE, one can explore 6578 natural compounds and 2566 fractional extracts isolated from 1952 distinct biological species including plants, marine organisms, fungi, and bacteria whose anticancer activities were validated with 1107 cell lines for 34 cancer types. Each entry in NPCARE is annotated with the cancer type, genus and species names of the biological resource, the cell line used for demonstrating the anticancer activity, PubChem ID, and a wealth of information about the target gene or protein. Besides the augmentation of plant entries up to 743 genus and 197 families, NPCARE is further enriched with the natural products and the fractional extracts of diverse non-traditional biological resources. Conclusions NPCARE is anticipated to serve as a dominant gateway for the discovery of new anticancer medicines due to the inclusion of a large number of the fractional extracts as well as the natural compounds isolated from a variety of biological resources. Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0188-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hwanho Choi
- Department of Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006 Korea
| | - Sun Young Cho
- College of Korean Medicine, Dongguk University, 27 Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326 Korea
| | - Ho Jeong Pak
- Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Sucho-gu, Seoul, 06591 Korea
| | - Youngsoo Kim
- Department of Biological Sciences, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Korea
| | - Jung-Yun Choi
- Graduate School of Medical Science and Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Korea
| | - Yoon Jae Lee
- Department of Korean Gynecology, Jaseng Hospital of Korean Medicine, 858 Eonju-ro, Gangnam-gu, Seoul, 06017 Korea
| | - Byung Hee Gong
- College of Korean Medicine, Wonkwang University, 460 Iksandae-ro, Iksan, Jeonbuk 54538 Korea
| | - Yeon Seok Kang
- College of Korean Medicine, Wonkwang University, 460 Iksandae-ro, Iksan, Jeonbuk 54538 Korea
| | - Taehoon Han
- WiFun Team, Nexon, 7 Pangyo-ro 256 gil, Bundang-gu, Seongnam-si, Gyeonggi-do 13487 Korea
| | - Geunbae Choi
- Hanvit Dental-Medical Hospital, 396 Seowon-daero, Wonju, Gangwon-do 26484 Korea
| | - Yeeun Cho
- Department of Clinical Korean Medicine, Kyung Hee University Korean Medicine Hospital, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447 Korea
| | - Soomin Lee
- Department of Clinical Korean Medicine, Kyung Hee University Korean Medicine Hospital, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447 Korea
| | - Dekwoo Ryoo
- Department of Clinical Korean Medicine, Kyung Hee University Korean Medicine Hospital, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447 Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006 Korea
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47
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Moloney MG. Natural Products as a Source for Novel Antibiotics. Trends Pharmacol Sci 2016; 37:689-701. [DOI: 10.1016/j.tips.2016.05.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 01/04/2023]
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48
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Li G, Zhang Z, Quan Q, Jiang R, Szeto SS, Yuan S, Wong WT, Lam HHC, Lee SMY, Chu IK. Discovery, Synthesis, and Functional Characterization of a Novel Neuroprotective Natural Product from the Fruit of Alpinia oxyphylla for use in Parkinson’s Disease Through LC/MS-Based Multivariate Data Analysis-Guided Fractionation. J Proteome Res 2016; 15:2595-606. [DOI: 10.1021/acs.jproteome.6b00152] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Guohui Li
- Department
of Chemistry, The University of Hong Kong, Hong Kong, China
- State
Key Laboratory of Quality Research in Chinese Medicine and Institute
of Chinese Medical Sciences, University of Macau, Avenue Padre
Tomás Pereira S.J., Taipa, Macao, China
| | - Zaijun Zhang
- State
Key Laboratory of Quality Research in Chinese Medicine and Institute
of Chinese Medical Sciences, University of Macau, Avenue Padre
Tomás Pereira S.J., Taipa, Macao, China
- Institute of New Drug Research, Guangdong Province Key Laboratory of Pharmacodynamic, Constituents of Traditional Chinese Medicine & New Drug Research, College of Pharmacy, Jinan University, Guangdong, China
| | - Quan Quan
- Department
of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Renwang Jiang
- Institute
of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Samuel S.W. Szeto
- Department
of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Shuai Yuan
- State
Key Laboratory of Quality Research in Chinese Medicine and Institute
of Chinese Medical Sciences, University of Macau, Avenue Padre
Tomás Pereira S.J., Taipa, Macao, China
| | - Wing-tak Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Herman H. C. Lam
- Department
of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Simon Ming-Yuen Lee
- State
Key Laboratory of Quality Research in Chinese Medicine and Institute
of Chinese Medical Sciences, University of Macau, Avenue Padre
Tomás Pereira S.J., Taipa, Macao, China
| | - Ivan K. Chu
- Department
of Chemistry, The University of Hong Kong, Hong Kong, China
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49
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Rodrigues T, Reker D, Schneider P, Schneider G. Counting on natural products for drug design. Nat Chem 2016; 8:531-41. [PMID: 27219696 DOI: 10.1038/nchem.2479] [Citation(s) in RCA: 717] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 02/12/2016] [Indexed: 02/08/2023]
Abstract
Natural products and their molecular frameworks have a long tradition as valuable starting points for medicinal chemistry and drug discovery. Recently, there has been a revitalization of interest in the inclusion of these chemotypes in compound collections for screening and achieving selective target modulation. Here we discuss natural-product-inspired drug discovery with a focus on recent advances in the design of synthetically tractable small molecules that mimic nature's chemistry. We highlight the potential of innovative computational tools in processing structurally complex natural products to predict their macromolecular targets and attempt to forecast the role that natural-product-derived fragments and fragment-like natural products will play in next-generation drug discovery.
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Affiliation(s)
- Tiago Rodrigues
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Daniel Reker
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Petra Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.,inSili.com LLC, Segantinisteig 3, 8049 Zürich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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50
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Abstract
Covering: up to 2015. Traditional Chinese medicine has played a significant role in the mainstream healthcare system in China for thousands of years. Here, we summarize 84 major compounds from 15 selected herbal medicines targeting neurodegenerative diseases. We present a perspective based on the analysis of physicochemical properties of these TCM compounds, and comparison with current drugs and candidates for the treatment of Parkinson's and Alzheimer's disease. The results demonstrate that traditional Chinese medicines contain compounds possessing physicochemical properties that have excellent overlap with developed western medicines.
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Affiliation(s)
- Chunping Tang
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia. and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China and Eskitis-SIMM Joint Laboratory for Drug Discovery, Australia
| | - Yunjiang Feng
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia. and Eskitis-SIMM Joint Laboratory for Drug Discovery, Australia
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia. and Eskitis-SIMM Joint Laboratory for Drug Discovery, Australia
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