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Ghosh R, Chakraborty A, Biswas A, Chowdhuri S. Computer aided identification of potential SARS CoV-2 main protease inhibitors from diterpenoids and biflavonoids of Torreya nucifera leaves. J Biomol Struct Dyn 2022; 40:2647-2662. [PMID: 33140695 PMCID: PMC7663460 DOI: 10.1080/07391102.2020.1841680] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022]
Abstract
SARS CoV-2 is the causative agent of the pandemic disease COVID-19. There is an urgent need for effective drugs or vaccines which can effectively combat this outbreak. The main protease (Mpro), a key component for the SARS CoV-2 replication, is considered to be one of the important drug targets for developing anti-COVID-19 drugs. This SARS CoV-2 Mpro/cysteine protease has high sequence similarity with the same protease from SARS CoV-1. Previously, it has been shown experimentally that eight diterpenoids and four biflavonoids derived from the leaf of Torreya nucifera show inhibitory effect on the cleavage/catalytic activity of the SARS CoV-1 Mpro. But whether these phytochemicals exhibit any inhibitory effect on SARS CoV-2 Mpro is unclear. To understand this fact, here, we have adopted various in-silico approaches. Diterpenoids and biflavonoids those qualified pharmacological test (hinokiol, amentoflavone, bilobetin and ginkgetin) and two well-known Mpro inhibitors (N3 and lopinavir) were subjected for molecular docking studies. Only three biflavonoids (amentoflavone, bilobetin and ginkgetin) were selected by comparing their binding affinities with N3 and lopinavir. They interacted with two most important catalytic residues of Mpro (His41 and Cys145). Molecular dynamics studies further revealed that these three Mpro-biflavonoid complexes are highly stable and share a similar degree of compactness. Besides, these complexes experience less conformational fluctuations and more expansion than Mpro-N3 and/or Mpro-lopinavir complex. MM-GBSA and H-bond analysis further corroborated these findings. Altogether, our study suggested that these three biflavonoids could possibly inhibit the proteolytic/catalytic activity of SARS CoV-2 Mpro and might be useful for COVID-19 treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ayon Chakraborty
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Ashis Biswas
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
| | - Snehasis Chowdhuri
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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2
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Ebob OT, Babiaka SB, Ntie-Kang F. Natural Products as Potential Lead Compounds for Drug Discovery Against SARS-CoV-2. NATURAL PRODUCTS AND BIOPROSPECTING 2021; 11:611-628. [PMID: 34515981 PMCID: PMC8435765 DOI: 10.1007/s13659-021-00317-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/01/2021] [Indexed: 05/09/2023]
Abstract
For the past 2 years, the coronavirus responsible for the COVID-19 infection has become a world pandemic, ruining the lives and economies of several nations in the world. This has scaled up research on the virus and the resulting infection with the goal of developing new vaccines and therapies. Natural products are known to be a rich source of lead compounds for drug discovery, including against infectious diseases caused by microbes (viruses, bacteria and fungi). In this review article, we conducted a literature survey aimed at identifying natural products with inhibitory concentrations against the coronaviruses or their target proteins, which lie below 10 µM. This led to the identification of 42 compounds belonging to the alkaloid, flavonoid, terpenoid, phenolic, xanthone and saponin classes. The cut off concentration of 10 µM was to limit the study to the most potent chemical entities, which could be developed into therapies against the viral infection to make a contribution towards limiting the spread of the disease.
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Affiliation(s)
- Oyere Tanyi Ebob
- Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Smith B. Babiaka
- Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Fidele Ntie-Kang
- Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon
- Institute for Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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3
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Fakhri S, Mohammadi Pour P, Piri S, Farzaei MH, Echeverría J. Modulating Neurological Complications of Emerging Infectious Diseases: Mechanistic Approaches to Candidate Phytochemicals. Front Pharmacol 2021; 12:742146. [PMID: 34764869 PMCID: PMC8576094 DOI: 10.3389/fphar.2021.742146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/23/2021] [Indexed: 12/02/2022] Open
Abstract
Growing studies are revealing the critical manifestations of influenza, dengue virus (DENV) infection, Zika virus (ZIKV) disease, and Ebola virus disease (EVD) as emerging infectious diseases. However, their corresponding mechanisms of major complications headed for neuronal dysfunction are not entirely understood. From the mechanistic point of view, inflammatory/oxidative mediators are activated during emerging infectious diseases towards less cell migration, neurogenesis impairment, and neuronal death. Accordingly, the virus life cycle and associated enzymes, as well as host receptors, cytokine storm, and multiple signaling mediators, are the leading players of emerging infectious diseases. Consequently, chemokines, interleukins, interferons, carbohydrate molecules, toll-like receptors (TLRs), and tyrosine kinases are leading orchestrates of peripheral and central complications which are in near interconnections. Some of the resulting neuronal manifestations have attracted much attention, including inflammatory polyneuropathy, encephalopathy, meningitis, myelitis, stroke, Guillain-Barré syndrome (GBS), radiculomyelitis, meningoencephalitis, memory loss, headaches, cranial nerve abnormalities, tremor, and seizure. The complex pathophysiological mechanism behind the aforementioned complications urges the need for finding multi-target agents with higher efficacy and lower side effects. In recent decades, the natural kingdom has been highlighted as promising neuroprotective natural products in modulating several dysregulated signaling pathways/mediators. The present study provides neuronal manifestations of some emerging infectious diseases and underlying pathophysiological mechanisms. Besides, a mechanistic-based strategy is developed to introduce candidate natural products as promising multi-target agents in combating major dysregulated pathways towards neuroprotection in influenza, DENV infection, ZIKV disease, and EVD.
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Affiliation(s)
- Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pardis Mohammadi Pour
- Department of Pharmacognosy, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sana Piri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Hosein Farzaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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Cataneo AHD, Ávila EP, Mendes LADO, de Oliveira VG, Ferraz CR, de Almeida MV, Frabasile S, Duarte Dos Santos CN, Verri WA, Bordignon J, Wowk PF. Flavonoids as Molecules With Anti- Zika virus Activity. Front Microbiol 2021; 12:710359. [PMID: 34566915 PMCID: PMC8462986 DOI: 10.3389/fmicb.2021.710359] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/03/2021] [Indexed: 11/13/2022] Open
Abstract
Zika virus (ZIKV) is an arthropod-born virus that is mainly transmitted to humans by mosquitoes of the genus Aedes spp. Since its first isolation in 1947, only a few human cases had been described until large outbreaks occurred on Yap Island (2007), French Polynesia (2013), and Brazil (2015). Most ZIKV-infected individuals are asymptomatic or present with a self-limiting disease and nonspecific symptoms such as fever, myalgia, and headache. However, in French Polynesia and Brazil, ZIKV outbreaks led to the diagnosis of congenital malformations and microcephaly in newborns and Guillain-Barré syndrome (GBS) in adults. These new clinical presentations raised concern from public health authorities and highlighted the need for anti-Zika treatments and vaccines to control the neurological damage caused by the virus. Despite many efforts in the search for an effective treatment, neither vaccines nor antiviral drugs have become available to control ZIKV infection and/or replication. Flavonoids, a class of natural compounds that are well-known for possessing several biological properties, have shown activity against different viruses. Additionally, the use of flavonoids in some countries as food supplements indicates that these molecules are nontoxic to humans. Thus, here, we summarize knowledge on the use of flavonoids as a source of anti-ZIKV molecules and discuss the gaps and challenges in this area before these compounds can be considered for further preclinical and clinical trials.
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Affiliation(s)
| | - Eloah Pereira Ávila
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | | | | | - Camila Rodrigues Ferraz
- Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Sandra Frabasile
- Sección Virologia, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | | | - Waldiceu Aparecido Verri
- Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Juliano Bordignon
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Brazil
| | - Pryscilla Fanini Wowk
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Brazil
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Toropov AA, Toropova AP, Benfenati E. The QSAR-search of effective agents towards coronaviruses applying the Monte Carlo method. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:689-698. [PMID: 34293992 DOI: 10.1080/1062936x.2021.1952649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Perhaps there is some similarity between the coronavirus of 2017 and the COVID-19. Consequently, a predictive model for the antiviral activity for the Middle East respiratory syndrome coronavirus (MERS-CoV, 2017) could be useful for designing the strategy and tactics in the struggle with coronaviruses in general and with COVID 19 in particular. Quantitative structure-activity relationships (QSARs) of inhibitory activity to MERS-CoV were developed. The index of ideality of correlation was applied to build up these models for the antiviral activity. The statistical quality of the best model is quite good (r2 = 0.84). A mechanistic interpretation of these models based on the molecular features with strong positive (i.e. promoters for endpoint increase) and strong negative (i.e. promoters for endpoint decrease) influence on the inhibitory activity is suggested. A collection of possible biologically active compounds, constructed using data on the above molecular features which are statistically reliable promoters of increase or decrease of the activity, is presented.
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Affiliation(s)
- A A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - A P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - E Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
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6
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Toropova AP, Toropov AA. Can the Monte Carlo method predict the toxicity of binary mixtures? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:39493-39500. [PMID: 33755888 DOI: 10.1007/s11356-021-13460-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Risk assessment of toxicants mainly is a result of experiments with single substances. However, toxicity in natural ecosystems typically does not result from single toxicant exposure but is rather a result of exposure to mixtures of toxicants. It is not surprising a mixture of toxicity is a subject of eco-toxicological interest for several decades. A quantitative structure-activity relationships (QSAR)-based approach is an attractive approach to assessing the joint effects in the binary mixtures. The validity of the proposed approach was demonstrated by comparing the predicted values against the experimentally determined values. Simplified molecular input-line entry system (SMILES) is used for the representation of the molecular structures of components of two-component mixtures to build up QSAR. The SMILES-based models are improving if the Monte Carlo optimization aimed to define 2D-optimal descriptors apply the so-called index of ideality of correlation (IIC), which is a mathematical function of both the correlation coefficient and mean absolute error calculated for the positive and negative difference between observed and calculated values of toxicity. The average statistical quality of these models (for the validation set) is n=25, R2=0.95, and RMSE=0.375.
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Affiliation(s)
- Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri, 2, 20156, Milano, Italy.
| | - Andrey A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri, 2, 20156, Milano, Italy
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7
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Abstract
Amentoflavone is one of the flavonoids that are known for their antiviral effects and many of them are predicted to have inhibitory effects against severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome Coronavirus (MERS-CoV) enzymes 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro). Amentoflavone is a biflavonoid found in the herbal extracts of St. John's wort (Hypericum perforatum), Gingko biloba, Selaginella tamariscina, Torreya nucifera, and many other plants. Its pharmacological actions have been listed as antiviral, antibacterial, antioxidant, anti-inflammatory, antidiabetic, antidepressant, and neuroprotective. Molecular docking studies have found that amentoflavone binds strongly to the active site of the main protease (Mpro) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). As conventional antiviral medications are met with limited success against coronavirus disease-2019 (COVID-19) and vaccines are one of the only weapons against COVID-19 in the pharmaceutical armamentarium, traditional medicines are being considered for the forefront battle against COVID-19. Clinical studies with Hypericum and Gingko extract as additional or alternative drugs/supplements are registered. Here we review the potential of amentoflavone, an active agent in both Hypericum and Gingko extract as an adjunct therapy for COVID-19. Its anti-inflammatory, antioxidant, and sepsis preventive actions could provide protection against the "cytokine storm." Compared with the herbal extracts, which induce cytochrome P450 (CYP) and uridine 5'-diphospho (UDP)-glucuronosyltransferases (UGT) activity producing a negative herb-drug interaction, amentoflavone is a potent inhibitor of CYP3A4, CYP2C9, and UGT. Further studies into the therapeutic potential of amentoflavone against the coronavirus infection are warranted.
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Affiliation(s)
- Akhilesh Vikram Singh
- School of Epidemiology and Public Health, Datta Meghe Institute of Medical Sciences, Sawangi (Meghe), Wardha, Maharashtra442004, India
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8
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Korn D, Pervitsky V, Bobrowski T, Alves VM, Schmitt C, Bizon C, Baker N, Chirkova R, Cherkasov A, Muratov E, Tropsha A. COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:13289222. [PMID: 33269341 PMCID: PMC7709174 DOI: 10.26434/chemrxiv.13289222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Revised: 11/26/2020] [Indexed: 12/02/2022]
Abstract
Objective: The COVID-19 pandemic has catalyzed a widespread effort to identify drug candidates and biological targets of relevance to SARS-COV-2 infection, which resulted in large numbers of publications on this subject. We have built the COVID-19 Knowledge Extractor (COKE), a web application to extract, curate, and annotate essential drug-target relationships from the research literature on COVID-19 to assist drug repurposing efforts. Materials and Methods: SciBiteAI ontological tagging of the COVID Open Research Dataset (CORD-19), a repository of COVID-19 scientific publications, was employed to identify drug-target relationships. Entity identifiers were resolved through lookup routines using UniProt and DrugBank. A custom algorithm was used to identify co-occurrences of protein and drug terms, and confidence scores were calculated for each entity pair. Results: COKE processing of the current CORD-19 database identified about 3,000 drug-protein pairs, including 29 unique proteins and 500 investigational, experimental, and approved drugs. Some of these drugs are presently undergoing clinical trials for COVID-19. Discussion: The rapidly evolving situation concerning the COVID-19 pandemic has resulted in a dramatic growth of publications on this subject in a short period. These circumstances call for methods that can condense the literature into the key concepts and relationships necessary for insights into SARS-CoV-2 drug repurposing. Conclusion: The COKE repository and web application deliver key drug - target protein relationships to researchers studying SARS-CoV-2. COKE portal may provide comprehensive and critical information on studies concerning drug repurposing against COVID-19. COKE is freely available at https://coke.mml.unc.edu/ and the code is available at https://github.com/DnlRKorn/CoKE.
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Affiliation(s)
- Daniel Korn
- Department of Computer Science, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Vera Pervitsky
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Vinicius M. Alves
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Charles Schmitt
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Chris Bizon
- Renaissance Computing Institute, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7568, USA
| | - Nancy Baker
- ParlezChem, 123 W Union Street, Hillsborough, NC, 27278, USA
| | - Rada Chirkova
- Department of Computer Science, North Carolina State University, Raleigh, NC, 27606-5550
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Wang L, Song J, Liu A, Xiao B, Li S, Wen Z, Lu Y, Du G. Research Progress of the Antiviral Bioactivities of Natural Flavonoids. NATURAL PRODUCTS AND BIOPROSPECTING 2020; 10:271-283. [PMID: 32948973 PMCID: PMC7500501 DOI: 10.1007/s13659-020-00257-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/24/2020] [Indexed: 05/05/2023]
Abstract
Flavonoids are now considered as an indispensable component in a variety of nutraceutical and pharmaceutical applications. Most recent researches have focused on the health aspects of flavonoids for humans. Especially, different flavonoids have been investigated for their potential antiviral activities, and several natural flavonoids exhibited significant antiviral properties both in vitro and in vivo. This review provides a survey of the literature regarding the evidence for antiviral bioactivities of natural flavonoids, highlights the cellular and molecular mechanisms of natural flavonoids on viruses, and presents the details of most reported flavonoids. Meanwhile, future perspectives on therapeutic applications of flavonoids against viral infections were discussed.
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Affiliation(s)
- Lin Wang
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Junke Song
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Ailin Liu
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Bin Xiao
- Laboratory of Clinical Pharmacy, Ordos Central Hospital, Ordos School of Clinical Medicine, Inner Mongolia Medical University, Ordos, 017000, China
| | - Sha Li
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Zhang Wen
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Yang Lu
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China
| | - Guanhua Du
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Xian Nong Tan Street, Beijing, 100050, China.
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10
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Toropov AA, Toropova AP, Veselinović AM, Leszczynska D, Leszczynski J. SARS-CoV M pro inhibitory activity of aromatic disulfide compounds: QSAR model. J Biomol Struct Dyn 2020; 40:780-786. [PMID: 32907512 PMCID: PMC7544941 DOI: 10.1080/07391102.2020.1818627] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The main protease (Mpro) of SARS-associated coronavirus (SARS-CoV) had caused a high rate of mortality in 2003. Current events (2019-2020) substantiate important challenges for society due to coronaviruses. Consequently, advancing models for the antiviral activity of therapeutic agents is a necessary component of the fast development of treatment for the virus. An analogy between anti-SARS agents suggested in 2017 and anti-coronavirus COVID-19 agents are quite probable. Quantitative structure-activity relationships for SARS-CoV are developed and proposed in this study. The statistical quality of these models is quite good. Mechanistic interpretation of developed models is based on the statistical and probability quality of molecular alerts extracted from SMILES. The novel, designed structures of molecules able to possess anti-SARS activities are suggested. For the final assessment of the designed molecules inhibitory potential, developed from the obtained QSAR model, molecular docking studies were applied. Results obtained from molecular docking studies were in a good correlation with the results obtained from QSAR modeling.
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Affiliation(s)
- Andrey A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | | | - Danuta Leszczynska
- Departments of Civil and Environmental Engineering, Jackson State University, Jackson, MS, USA
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, MS, USA
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11
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The anti-Zika virus and anti-tumoral activity of the citrus flavanone lipophilic naringenin-based compounds. Chem Biol Interact 2020; 331:109218. [PMID: 32916141 DOI: 10.1016/j.cbi.2020.109218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
Flavonoids are natural products widely recognized for their plurality of applications such as antiviral, antiproliferative, antitumor activities and, antioxidant properties. The flavanone naringenin is presented in citrus fruits and has been studied to combat recurrent diseases that still lack effective treatment. Research groups have been investing efforts to the development of new, safe and active candidates to combat these agents or conditions and despite good results recently reported against the Zika virus (ZIKV) and tumor cells, the use of citrus naringenin is limited due to its low bioavailability. Structural exchanges through functionalization, for example, attaching lipophilic groups instead of hydroxyl groups, can further enhance biological properties. Here, the synthesis and characterization of regioselective naringenin mono-7-O-ethers and both mono and di-fatty acid esters, structurally lipophilic ones were demonstrated. Finally, in vitro studies of anti-ZIKV action and antiproliferative activities against melanoma (B16-F10) and breast carcinoma (4T1) cells showed the ether derivatives were actives, with IC50 ranging from 6.76, 18.5 and 22.6 μM to 28.53, 45.1 and 32.3 μM referring to ZIKV, B16-F10 and 4T1 cell lines, respectively. The lipophilic ethers present the ability to inhibit selectively ZIKV-replication in human cells and inhibitions. This class of modifications in flavonoid molecules could be further explore in the future development of specific anti-ZIKV compounds.
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12
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Hossein F. An overview of the current medical literature on Zika virus. Biophys Rev 2020; 12:1133-1138. [PMID: 32880054 DOI: 10.1007/s12551-020-00748-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
Zika virus is a member of the family of Flaviviridae, which is primarily spread to humans by mosquito bites. It has been linked to microcephaly in neonates, and as such, it poses a significant risk to human pregnancy. Zika virus infection is also implicated in other severe neurological disorders such as Guillain-Barre syndrome. There is currently no vaccine available to treat Zika virus disease, and as such, it represents a serious challenge to public health. Antigenic similarities between Zika and dengue can suggest artificially high infection rates of Zika within specific population groups. Here, we review recent literature and provide an update on the status of the Zika outbreak, including a description of available medical countermeasure options and current diagnosis methodology.
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Affiliation(s)
- Fria Hossein
- School of Engineering, Nanotechnology and Integrated Bio-Engineering Centre (NIBEC), Ulster University, Shore Road, BT37 0QB, Newtownabbey, United Kingdom.
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13
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Zivkovic M, Zlatanovic M, Zlatanovic N, Golubović M, Veselinović AM. The Application of the Combination of Monte Carlo Optimization Method based QSAR Modeling and Molecular Docking in Drug Design and Development. Mini Rev Med Chem 2020; 20:1389-1402. [DOI: 10.2174/1389557520666200212111428] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 01/18/2023]
Abstract
In recent years, one of the promising approaches in the QSAR modeling Monte Carlo optimization
approach as conformation independent method, has emerged. Monte Carlo optimization has
proven to be a valuable tool in chemoinformatics, and this review presents its application in drug discovery
and design. In this review, the basic principles and important features of these methods are discussed
as well as the advantages of conformation independent optimal descriptors developed from the
molecular graph and the Simplified Molecular Input Line Entry System (SMILES) notation compared
to commonly used descriptors in QSAR modeling. This review presents the summary of obtained results
from Monte Carlo optimization-based QSAR modeling with the further addition of molecular
docking studies applied for various pharmacologically important endpoints. SMILES notation based
optimal descriptors, defined as molecular fragments, identified as main contributors to the increase/
decrease of biological activity, which are used further to design compounds with targeted activity
based on computer calculation, are presented. In this mini-review, research papers in which molecular
docking was applied as an additional method to design molecules to validate their activity further,
are summarized. These papers present a very good correlation among results obtained from Monte
Carlo optimization modeling and molecular docking studies.
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Affiliation(s)
| | | | | | - Mladjan Golubović
- Clinic for Anesthesiology and Intensive Care, Clinical Center Nis, Nis, Serbia
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14
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Xiang C, Cao M, Miao A, Gao F, Li X, Pan G, Zhang W, Zhang Y, Yu P, Teng Y. Antioxidant activities of anastatin A & B derivatives and compound 38c's protective effect in a mouse model of CCl 4-induced acute liver injury. RSC Adv 2020; 10:14337-14346. [PMID: 35498475 PMCID: PMC9051925 DOI: 10.1039/d0ra00822b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/26/2020] [Indexed: 12/15/2022] Open
Abstract
Anastatins A and B, two flavonoid compounds isolated from desert plant Anastatica hierochuntica, have protective activities for primary rat hepatocytes. Anastatins A and B, and their derivatives, were synthesized by our group previously. In this study, the antioxidant activity and cytotoxicity of these compounds were studied using chemical assessment methods, cell proliferation inhibition experiments, and cell oxidative damage models. The best compound, 38c, was used to study the hepatoprotection activity and mechanism by using a CCl4-induced liver injury model in mice. The results show that most of these flavonoid compounds have good antioxidant activity and low cytotoxicity in vitro. Among them, the most potent compound was 38c, which exhibited a protective effect on CCl4-induced hepatic injury by suppressing the amount of CYP2E1. These findings indicate that anastatin flavonoid derivatives have potential therapeutic utility against oxidative hepatic injury.
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Affiliation(s)
- Cen Xiang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
| | - Menglin Cao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
| | - Ai Miao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
| | - Feng Gao
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
| | - Xuzhe Li
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
| | - Guojun Pan
- School of Life Sciences, Shandong First Medical University, Shandong Academy of Medical Sciences Changcheng Road 619 Tai'an City 271000 Shandong province China
| | - Wenqiang Zhang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
| | - Yongmin Zhang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
- Sorbonne Université, Institut Parisien de Chimie Moléculaire, UMR8232 CNRS 4 Place Jussieu 75005 Paris France
| | - Peng Yu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
| | - Yuou Teng
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology Tianjin 300457 China
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15
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Toropov AA, Toropova AP. QSPR/QSAR: State-of-Art, Weirdness, the Future. Molecules 2020; 25:E1292. [PMID: 32178379 PMCID: PMC7143984 DOI: 10.3390/molecules25061292] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
Ability of quantitative structure-property/activity relationships (QSPRs/QSARs) to serve for epistemological processes in natural sciences is discussed. Some weirdness of QSPR/QSAR state-of-art is listed. There are some contradictions in the research results in this area. Sometimes, these should be classified as paradoxes or weirdness. These points are often ignored. Here, these are listed and briefly commented. In addition, hypotheses on the future evolution of the QSPR/QSAR theory and practice are suggested. In particular, the possibility of extending of the QSPR/QSAR problematic by searching for the "statistical similarity" of different endpoints is suggested and illustrated by an example for relatively "distanced each from other" endpoints, namely (i) mutagenicity, (ii) anticancer activity, and (iii) blood-brain barrier.
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Affiliation(s)
| | - Alla P. Toropova
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Science, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy;
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16
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Mondal D, Ghosh K, Baidya ATK, Gantait AM, Gayen S. Identification of structural fingerprints for in vivo toxicity by using Monte Carlo based QSTR modeling of nitroaromatics. Toxicol Mech Methods 2020; 30:257-265. [DOI: 10.1080/15376516.2019.1709238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Dipayan Mondal
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. HarisinghGour University, Sagar, Madhya Pradesh, India
| | - Kalyan Ghosh
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. HarisinghGour University, Sagar, Madhya Pradesh, India
| | - Anurag T. K. Baidya
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. HarisinghGour University, Sagar, Madhya Pradesh, India
| | | | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. HarisinghGour University, Sagar, Madhya Pradesh, India
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17
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Jain S, Amin SA, Adhikari N, Jha T, Gayen S. Good and bad molecular fingerprints for human rhinovirus 3C protease inhibition: identification, validation, and application in designing of new inhibitors through Monte Carlo-based QSAR study. J Biomol Struct Dyn 2020; 38:66-77. [PMID: 30646829 DOI: 10.1080/07391102.2019.1566093] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/01/2019] [Indexed: 01/12/2023]
Abstract
HRV 3 C protease (HRV 3Cpro) is an important target for common cold and upper respiratory tract infection. Keeping in view of the non-availability of drug for the treatment, newer computer-based modelling strategies should be applied to rationalize the process of antiviral drug discovery in order to decrease the valuable time and huge expenditure of the process. The present work demonstrates a structure wise optimization using Monte Carlo-based QSAR method that decomposes ligand compounds (in SMILES format) into several molecular fingerprints/descriptors. The current state-of-the-art in QSAR study involves the balance of correlation approach using four different sets: training, invisible training, calibration, and validation. The final models were also validated through mean absolute error, index of ideality of correlation, Y-randomization and applicability domain analysis. R2 and Q2 values for the best model were 0.8602, 0.8507 (training); 0.8435, 0.8331 (invisible training); 0.7424, 0.7020 (calibration); 0.5993, 0.5216 (validation), respectively. The process identified some molecular substructures as good and bad fingerprints depending on their effect to increase or decrease the HRV 3Cpro inhibition. Finally, new inhibitors were designed based on the fundamental concept to replace the bad fragments with the good fragments as well as including more good fragments into the structure. The study points out the importance of the fingerprint based drug design strategy through Monte Carlo optimization method in the modelling of HRV 3Cpro inhibitors.
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Affiliation(s)
- Sanskar Jain
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, India
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18
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Santos FRS, Nunes DAF, Lima WG, Davyt D, Santos LL, Taranto AG, M. S. Ferreira J. Identification of Zika Virus NS2B-NS3 Protease Inhibitors by Structure-Based Virtual Screening and Drug Repurposing Approaches. J Chem Inf Model 2019; 60:731-737. [DOI: 10.1021/acs.jcim.9b00933] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Felipe R. S. Santos
- Laboratório de Microbiologia Médica, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del-Rei (UFSJ), Divinópolis 35501-296, Minas Gerais, Brasil
- Laboratório de Química Farmacêutica Medicinal, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del-Rei (UFSJ), Divinópolis 35501-296, Minas Gerais, Brasil
| | - Damiana A. F. Nunes
- Laboratório de Microbiologia Médica, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del-Rei (UFSJ), Divinópolis 35501-296, Minas Gerais, Brasil
| | - William G. Lima
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brasil
| | - Danilo Davyt
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
| | - Luciana L. Santos
- Laboratório de Biologia Molecular, Campus Centro-Oeste Dona Lindu, Universidade Federal de São, João Del-Rei (UFSJ), Divinópolis 35501-296, Minas Gerais, Brasil
| | - Alex G. Taranto
- Laboratório de Química Farmacêutica Medicinal, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del-Rei (UFSJ), Divinópolis 35501-296, Minas Gerais, Brasil
| | - Jaqueline M. S. Ferreira
- Laboratório de Microbiologia Médica, Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del-Rei (UFSJ), Divinópolis 35501-296, Minas Gerais, Brasil
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19
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Cataneo AHD, Kuczera D, Koishi AC, Zanluca C, Silveira GF, Arruda TBD, Suzukawa AA, Bortot LO, Dias-Baruffi M, Verri WA, Robert AW, Stimamiglio MA, Duarte Dos Santos CN, Wowk PF, Bordignon J. The citrus flavonoid naringenin impairs the in vitro infection of human cells by Zika virus. Sci Rep 2019; 9:16348. [PMID: 31705028 PMCID: PMC6841724 DOI: 10.1038/s41598-019-52626-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/16/2019] [Indexed: 12/16/2022] Open
Abstract
The Zika virus (ZIKV) is an arthropod-borne virus that belongs to the Flaviviridae family. The ZIKV infection is usually asymptomatic or is associated with mild clinical manifestations; however, increased numbers of cases of microcephaly and birth defects have been recently reported. To date, neither a vaccine nor an antiviral treatment has become available to control ZIKV replication. Among the natural compounds recognized for their medical properties, flavonoids, which can be found in fruits and vegetables, have been found to possess biological activity against a variety of viruses. Here, we demonstrate that the citrus flavanone naringenin (NAR) prevented ZIKV infection in human A549 cells in a concentration-dependent and ZIKV-lineage independent manner. NAR antiviral activity was also observed when primary human monocyte-derived dendritic cells were infected by ZIKV. NAR displayed its antiviral activity when the cells were treated after infection, suggesting that NAR acts on the viral replication or assembly of viral particles. Moreover, a molecular docking analysis suggests a potential interaction between NAR and the protease domain of the NS2B-NS3 protein of ZIKV which could explain the anti-ZIKV activity of NAR. Finally, the results support the potential of NAR as a suitable candidate molecule for developing anti-ZIKV treatments.
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Affiliation(s)
| | - Diogo Kuczera
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Andrea Cristine Koishi
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | | | - Thais Bonato de Arruda
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Andréia Akemi Suzukawa
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Leandro Oliveira Bortot
- Laboratório de Física Biológica, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marcelo Dias-Baruffi
- Laboratório de Glicoimunologia, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Waldiceu Aparecido Verri
- Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Paraná, Brazil
| | - Anny Waloski Robert
- Laboratório de Células Tronco, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | | | | | - Pryscilla Fanini Wowk
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil.
| | - Juliano Bordignon
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil.
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20
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Antiviral Efficacy of Flavonoids against Enterovirus 71 Infection in Vitro and in Newborn Mice. Viruses 2019; 11:v11070625. [PMID: 31284698 PMCID: PMC6669683 DOI: 10.3390/v11070625] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 12/26/2022] Open
Abstract
Enterovirus 71 (EV71) infection is known to cause hand, foot, and mouth disease (HFMD), which is associated with neurological complications; however, there is currently no effective treatment for this infection. Flavonoids are a large group of naturally occurring compounds with multiple bioactivities, and the inhibitory effects of several flavonoids against EV71 have been studied in cell cultures; however, to date, there are no reported data on their effects in animal models. In this study, we confirmed the in vitro activities of eight flavonoids against EV71 infection, based on the inhibition of cytopathic effects. Moreover, these flavonoids were found to reduce viral genomic RNA replication and protein synthesis. We further demonstrated the protective efficacy of these flavonoids in newborn mice challenged with a lethal dose of EV71. Apigenin, luteolin, kaempferol, formononetin, and penduletin conferred survival protection of 88.89%, 91.67%, 88.89%, 75%, and 66.67%, respectively, from the lethal EV71 challenge. In addition, isorhamnetin provided the highest mice survival protection of 100% at a dose of 10 mg/kg. This study, to the best of our knowledge, is the first to evaluate the in vivo anti-EV7l activities of multiple flavonoids, and we accordingly identified flavonoids as potential leading compounds for anti-EV71 drug development.
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21
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Jain S, Bhardwaj B, Amin SA, Adhikari N, Jha T, Gayen S. Exploration of good and bad structural fingerprints for inhibition of indoleamine-2,3-dioxygenase enzyme in cancer immunotherapy using Monte Carlo optimization and Bayesian classification QSAR modeling. J Biomol Struct Dyn 2019; 38:1683-1696. [PMID: 31057090 DOI: 10.1080/07391102.2019.1615000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Indoleamine-2,3-dioxygenase 1 (IDO1) is an extrahepatic, heme-containing and tryptophan-catalyzing enzyme responsible for causing blockade of T-cell proliferation and differentiation by depleting tryptophan level in cancerous cells. Therefore, inhibition of IDO1 may be a useful strategy for immunotherapy against cancer. In this study, 448 structurally diverse IDO1 inhibitors with a wide range of activity has been taken into consideration for classification QSAR analysis through Monte Carlo Optimization by using different splits as well as different combinations of SMILES-based, graph-based and hybrid descriptors. The best model from Monte Carlo optimization was interpreted to find out the good and bad structural fingerprints for IDO1 and further justified by using Bayesian classification QSAR modeling. Among the three splits in Monte Carlo optimization, the statistics of the best model was obtained from Split 3: sensitivity = 0.87, specificity = 0.91, accuracy = 0.89 and MCC = 0.78. In Bayesian classification modeling, the ROC scores for training and test set were found to be 0.91 and 0.86, respectively. The combined modeling analysis revealed that the presence of aryl hydrazyl sulphonyl moiety, furazan ring, halogen substitution, nitro group and hetero atoms in aromatic system can be very useful in designing IDO1 inhibitors. All the good and bad structural fingerprints for IDO1 were identified and are justified by correlating these fragments to the inhibition of IDO1 enzyme. These structural fingerprints will guide the researchers in this field to design better inhibitors against IDO1 enzyme for cancer immunotherapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanskar Jain
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. HarisinghGour University, Sagar, Madhya Pradesh, India
| | - Bhagwati Bhardwaj
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. HarisinghGour University, Sagar, Madhya Pradesh, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal and Pharmaceutical Chemistry, Jadavpur University, Kolkata, West Bengal, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal and Pharmaceutical Chemistry, Jadavpur University, Kolkata, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Department of Pharmaceutical Technology, Division of Medicinal and Pharmaceutical Chemistry, Jadavpur University, Kolkata, West Bengal, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. HarisinghGour University, Sagar, Madhya Pradesh, India
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22
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Rocha TA, Moura DFD, Silva MMD, Dos Santos Souza TG, Lira MADCD, Barros DDM, da Silva AG, Ximenes RM, Falcão EPDS, Chagas CA, Júnior FCADA, Santos NPDS, Silva MVD, Correia MTDS. Evaluation of cytotoxic potential, oral toxicity, genotoxicity, and mutagenicity of organic extracts of Pityrocarpa moniliformis. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2019; 82:216-231. [PMID: 30849290 DOI: 10.1080/15287394.2019.1576563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The objective of this study was to determine the cytotoxicity of organic extracts of P. moniliformis in vitro and identify the acute toxicity and genotoxicity in vivo. The leaves were extracted using three organic solvents (cyclohexane [EP1], ethyl acetate [EP2], and methanol [EP3]). Phytochemical qualitative analysis was performed by thin layer chromatography (TLC). Cytotoxicity tests were performed on human embryonic kidney (HEK) cells and J774 murine macrophages. Acute toxicity in mice was measured after intraperitoneal (ip) administration of 2000 mg/kg, while evaluation of genotoxicity and mutagenicity were assessed using the comet assay and the micronucleus (MN) test, respectively. The TLC analysis of the extracts revealed the presence of flavonoids, triterpenes, steroids, and saponins. In the cytotoxicity assay, extracts EP1 and EP3 altered proliferation of HEK cells, and all organic extracts increased the viability of J774 cells. In the toxicity tests, no deaths or behavioral alterations were observed in mice exposed to the acute dose of the extracts. Although some extracts led to changes in hematological and histological parameters, these results did not indicate physiological changes. In relation to the MN test and comet assay, no significant changes were detected in the DNA of the animals tested with the extracts EP1, EP2, and EP3. Thus, extracts of P. moniliformis were not considered to be toxic and did not induce formation of MN or damage to cellular DNA in the genotoxicity tests.
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Affiliation(s)
- Tamiris Alves Rocha
- a Laboratório de Biologia Molecular, Departamento de Bioquímica , Universidade Federal de Pernambuco , Recife , Brazil
| | - Danielle Feijó de Moura
- a Laboratório de Biologia Molecular, Departamento de Bioquímica , Universidade Federal de Pernambuco , Recife , Brazil
| | - Marllyn Marques da Silva
- b Laboratório de Nanotecnologia, Biotecnologia e Cultura de Células (NANOBIOCEL), Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Brazil
| | - Talita Giselly Dos Santos Souza
- c Laboratório de Biotecnologia e Fármacos, Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Vitória de Santo Antão , Brazil
| | - Maria Aparecida da Conceição de Lira
- d Laboratório de Síntese e Isolamento Molecular (SIM). Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Vitória de Santo Antão
| | - Dayane de Melo Barros
- e Laboratório de Microbiologia de Alimentos, Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Brazil
| | - Alexandre Gomes da Silva
- f Departamento de Antibióticos , Universidade Federal de Pernambuco , Recife , Pernambuco , Brazil
- g Núcleo de Bioprospecção da Caatinga , Instituto Nacional do Semiárido , Paraíba , Brazil
| | - Rafael Matos Ximenes
- b Laboratório de Nanotecnologia, Biotecnologia e Cultura de Células (NANOBIOCEL), Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Brazil
| | - Emerson Peter da Silva Falcão
- d Laboratório de Síntese e Isolamento Molecular (SIM). Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Vitória de Santo Antão
| | - Cristiano Aparecido Chagas
- h Laboratório de Biotecnologia e Fármacos, Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Vitória de Santo Antão , Brazil
| | | | - Noêmia Pereira da Silva Santos
- b Laboratório de Nanotecnologia, Biotecnologia e Cultura de Células (NANOBIOCEL), Centro Acadêmico de Vitória , Universidade Federal de Pernambuco , Brazil
| | - Marcia Vanusa da Silva
- a Laboratório de Biologia Molecular, Departamento de Bioquímica , Universidade Federal de Pernambuco , Recife , Brazil
- g Núcleo de Bioprospecção da Caatinga , Instituto Nacional do Semiárido , Paraíba , Brazil
| | - Maria Tereza Dos Santos Correia
- a Laboratório de Biologia Molecular, Departamento de Bioquímica , Universidade Federal de Pernambuco , Recife , Brazil
- g Núcleo de Bioprospecção da Caatinga , Instituto Nacional do Semiárido , Paraíba , Brazil
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