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Gonzalez-Ponce K, Horta Andrade C, Hunter F, Kirchmair J, Martinez-Mayorga K, Medina-Franco JL, Rarey M, Tropsha A, Varnek A, Zdrazil B. School of cheminformatics in Latin America. J Cheminform 2023; 15:82. [PMID: 37726809 PMCID: PMC10507835 DOI: 10.1186/s13321-023-00758-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023] Open
Abstract
We report the major highlights of the School of Cheminformatics in Latin America, Mexico City, November 24-25, 2022. Six lectures, one workshop, and one roundtable with four editors were presented during an online public event with speakers from academia, big pharma, and public research institutions. One thousand one hundred eighty-one students and academics from seventy-nine countries registered for the meeting. As part of the meeting, advances in enumeration and visualization of chemical space, applications in natural product-based drug discovery, drug discovery for neglected diseases, toxicity prediction, and general guidelines for data analysis were discussed. Experts from ChEMBL presented a workshop on how to use the resources of this major compounds database used in cheminformatics. The school also included a round table with editors of cheminformatics journals. The full program of the meeting and the recordings of the sessions are publicly available at https://www.youtube.com/@SchoolChemInfLA/featured .
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Affiliation(s)
- Karla Gonzalez-Ponce
- Institute of Chemistry, Campus Merida, National Autonomous University of Mexico, Merida‑Tetiz Highway, Km. 4.5, Ucu, Yucatan, Mexico
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Goiania, GO, Brazil
| | - Fiona Hunter
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridgeshire, UK
| | - Johannes Kirchmair
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 2D 303, 1090, Vienna, Austria
| | - Karina Martinez-Mayorga
- Institute of Chemistry, Campus Merida, National Autonomous University of Mexico, Merida‑Tetiz Highway, Km. 4.5, Ucu, Yucatan, Mexico.
- Institute for Applied Mathematics and Systems, Merida Research Unit, National Autonomous University of Mexico, Sierra Papacal, Merida, Yucatan, Mexico.
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, 04510, Mexico City, Mexico.
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146, Hamburg, Germany
| | - Alexander Tropsha
- Molecular Modeling Laboratory, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandre Varnek
- Laboratoire d'Infochimie, UMR 7177 CNRS, Université de Strasbourg, 4, Rue B. Pascal, 67000, Strasbourg, France
| | - Barbara Zdrazil
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridgeshire, UK
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Durgam L, Pagag J, Indra Neela Y, Guruprasad L. Mutational analyses, pharmacophore-based inhibitor design and in silico validation for Zika virus NS3-helicase. J Biomol Struct Dyn 2023:1-19. [PMID: 37712848 DOI: 10.1080/07391102.2023.2252929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Zika virus is responsible for causing Zika infections and was declared as a public health emergency of international concern in February 2016. The Zika virus NS3-helicase is a viable drug target for the design of inhibitors due to its essential role in the replication of viral genome. The viral RNA is unwound by the NS3-helicase in order to enable the reproduction of viral genome by the NS5 protein. Zika virus infections in humans are being reported for the last 15 years. We have therefore carried out amino acid mutational analyses of NS3-helicase. NS3-helicase has two crucial binding sites: the ATP and RNA binding sites. The cofactor-ATP based pharmacophore was generated for virtual screening of ZINC database using Pharmit server, that is followed by molecular docking and molecular dynamics simulations of potential hits as probable Zika virus NS3-helicase inhibitors at the cofactor binding site. The drug-like properties of the molecules were analysed and, DFT calculations were performed on the five best molecules to reveal their stability in solvent phase compared to gas phase, the HOMO and LUMO and electrostatic potential maps to analyze the electronic and geometric characteristics. These are significant findings towards the discovery of new inhibitors of Zika virus NS3-helicase, a promising drug target to treat the Zika virus infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laxman Durgam
- School of Chemistry, University of Hyderabad, Hyderabad, India
| | - Jishu Pagag
- School of Chemistry, University of Hyderabad, Hyderabad, India
| | - Y Indra Neela
- School of Chemistry, University of Hyderabad, Hyderabad, India
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Mottin M, de Paula Sousa BK, de Moraes Roso Mesquita NC, de Oliveira KIZ, Noske GD, Sartori GR, de Oliveira Albuquerque A, Urbina F, Puhl AC, Moreira-Filho JT, Souza GE, Guido RV, Muratov E, Neves BJ, da Silva JHM, Clark AE, Siqueira-Neto JL, Perryman AL, Oliva G, Ekins S, Andrade CH. Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. J Chem Inf Model 2022; 62:6825-6843. [PMID: 36239304 PMCID: PMC9923514 DOI: 10.1021/acs.jcim.2c00596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Zika virus (ZIKV) is a neurotropic arbovirus considered a global threat to public health. Although there have been several efforts in drug discovery projects for ZIKV in recent years, there are still no antiviral drugs approved to date. Here, we describe the results of a global collaborative crowdsourced open science project, the OpenZika project, from IBM's World Community Grid (WCG), which integrates different computational and experimental strategies for advancing a drug candidate for ZIKV. Initially, molecular docking protocols were developed to identify potential inhibitors of ZIKV NS5 RNA-dependent RNA polymerase (NS5 RdRp), NS3 protease (NS2B-NS3pro), and NS3 helicase (NS3hel). Then, a machine learning (ML) model was built to distinguish active vs inactive compounds for the cytoprotective effect against ZIKV infection. We performed three independent target-based virtual screening campaigns (NS5 RdRp, NS2B-NS3pro, and NS3hel), followed by predictions by the ML model and other filters, and prioritized a total of 61 compounds for further testing in enzymatic and phenotypic assays. This yielded five non-nucleoside compounds which showed inhibitory activity against ZIKV NS5 RdRp in enzymatic assays (IC50 range from 0.61 to 17 μM). Two compounds thermally destabilized NS3hel and showed binding affinity in the micromolar range (Kd range from 9 to 35 μM). Moreover, the compounds LabMol-301 inhibited both NS5 RdRp and NS2B-NS3pro (IC50 of 0.8 and 7.4 μM, respectively) and LabMol-212 thermally destabilized the ZIKV NS3hel (Kd of 35 μM). Both also protected cells from death induced by ZIKV infection in in vitro cell-based assays. However, while eight compounds (including LabMol-301 and LabMol-212) showed a cytoprotective effect and prevented ZIKV-induced cell death, agreeing with our ML model for prediction of this cytoprotective effect, no compound showed a direct antiviral effect against ZIKV. Thus, the new scaffolds discovered here are promising hits for future structural optimization and for advancing the discovery of further drug candidates for ZIKV. Furthermore, this work has demonstrated the importance of the integration of computational and experimental approaches, as well as the potential of large-scale collaborative networks to advance drug discovery projects for neglected diseases and emerging viruses, despite the lack of available direct antiviral activity and cytoprotective effect data, that reflects on the assertiveness of the computational predictions. The importance of these efforts rests with the need to be prepared for future viral epidemic and pandemic outbreaks.
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Affiliation(s)
- Melina Mottin
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, 70910-900, Brazil
| | - Bruna Katiele de Paula Sousa
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | | | | | - Gabriela Dias Noske
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | | | | | - Fabio Urbina
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, 27606, USA
| | - Ana C. Puhl
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, 27606, USA
| | - José Teófilo Moreira-Filho
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | - Guilherme E. Souza
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | - Rafael V.C. Guido
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | - Eugene Muratov
- University of North Carolina - University of North Carolina at Chapel Hill, 27599, USA
- Universidade Federal de Paraíba, Joao Pessoa, PB, 58051-900, Brazil
| | - Bruno Junior Neves
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | | | - Alex E. Clark
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, USA
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, USA
| | - Alexander L. Perryman
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University–New Jersey Medical School, Newark, NJ 07103, United States
- Repare Therapeutics, 7210 Rue Frederick-Banting, Suite 100, Montreal, QC, H4S 2A1, Canada
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, 27606, USA
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
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Characterization of the RNA-dependent RNA polymerase from Chikungunya virus and discovery of a novel ligand as a potential drug candidate. Sci Rep 2022; 12:10601. [PMID: 35732685 PMCID: PMC9217121 DOI: 10.1038/s41598-022-14790-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of Chikungunya fever, an acute febrile and arthritogenic illness with no effective treatments available. The development of effective therapeutic strategies could be significantly accelerated with detailed knowledge of the molecular components behind CHIKV replication. However, drug discovery is hindered by our incomplete understanding of their main components. The RNA-dependent RNA-polymerase (nsP4-CHIKV) is considered the key enzyme of the CHIKV replication complex and a suitable target for antiviral therapy. Herein, the nsP4-CHIKV was extensively characterized through experimental and computational biophysical methods. In the search for new molecules against CHIKV, a compound designated LabMol-309 was identified as a strong ligand of the nsp4-CHIKV and mapped to bind to its active site. The antiviral activity of LabMol-309 was evaluated in cellular-based assays using a CHIKV replicon system and a reporter virus. In conclusion, this study highlights the biophysical features of nsP4-CHIKV and identifies a new compound as a promising antiviral agent against CHIKV infection.
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A step toward better sample management of COVID-19: On-spot detection by biometric technology and artificial intelligence. COVID-19 AND THE SUSTAINABLE DEVELOPMENT GOALS 2022. [PMCID: PMC9334987 DOI: 10.1016/b978-0-323-91307-2.00017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Borba JVVB, Silva AC, Lima MNN, Mendonca SS, Furnham N, Costa FTM, Andrade CH. Chemogenomics and bioinformatics approaches for prioritizing kinases as drug targets for neglected tropical diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 124:187-223. [PMID: 33632465 DOI: 10.1016/bs.apcsb.2020.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neglected tropical diseases (NTDs) are a group of twenty-one diseases classified by the World Health Organization that prevail in regions with tropical and subtropical climate and affect more than one billion people. There is an urgent need to develop new and safer drugs for these diseases. Protein kinases are a potential class of targets for developing new drugs against NTDs, since they play crucial role in many biological processes, such as signaling pathways, regulating cellular communication, division, metabolism and death. Bioinformatics is a field that aims to organize large amounts of biological data as well as develop and use tools for understanding and analyze them in order to produce meaningful information in a biological manner. In combination with chemogenomics, which analyzes chemical-biological interactions to screen ligands against selected targets families, these approaches can be used to stablish a rational strategy for prioritizing new drug targets for NTDs. Here, we describe how bioinformatics and chemogenomics tools can help to identify protein kinases and their potential inhibitors for the development of new drugs for NTDs. We present a review of bioinformatics tools and techniques that can be used to define an organisms kinome for drug prioritization, drug and target repurposing, multi-quinase inhibition approachs and selectivity profiling. We also present some successful examples of the application of such approaches in recent case studies.
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Affiliation(s)
- Joyce Villa Verde Bastos Borba
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil; Laboratory of Tropical Diseases-Prof. Luiz Jacintho da Silva, Department of Genetics, Evolution and Bioagents, University of Campinas, Campinas, SP, Brazil
| | - Arthur Carvalho Silva
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Marilia Nunes Nascimento Lima
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Sabrina Silva Mendonca
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases-Prof. Luiz Jacintho da Silva, Department of Genetics, Evolution and Bioagents, University of Campinas, Campinas, SP, Brazil
| | - Carolina Horta Andrade
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil; Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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7
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Lalmuanawma S, Hussain J, Chhakchhuak L. Applications of machine learning and artificial intelligence for Covid-19 (SARS-CoV-2) pandemic: A review. CHAOS, SOLITONS, AND FRACTALS 2020; 139:110059. [PMID: 32834612 PMCID: PMC7315944 DOI: 10.1016/j.chaos.2020.110059] [Citation(s) in RCA: 285] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND AND OBJECTIVE During the recent global urgency, scientists, clinicians, and healthcare experts around the globe keep on searching for a new technology to support in tackling the Covid-19 pandemic. The evidence of Machine Learning (ML) and Artificial Intelligence (AI) application on the previous epidemic encourage researchers by giving a new angle to fight against the novel Coronavirus outbreak. This paper aims to comprehensively review the role of AI and ML as one significant method in the arena of screening, predicting, forecasting, contact tracing, and drug development for SARS-CoV-2 and its related epidemic. METHOD A selective assessment of information on the research article was executed on the databases related to the application of ML and AI technology on Covid-19. Rapid and critical analysis of the three crucial parameters, i.e., abstract, methodology, and the conclusion was done to relate to the model's possibilities for tackling the SARS-CoV-2 epidemic. RESULT This paper addresses on recent studies that apply ML and AI technology towards augmenting the researchers on multiple angles. It also addresses a few errors and challenges while using such algorithms in real-world problems. The paper also discusses suggestions conveying researchers on model design, medical experts, and policymakers in the current situation while tackling the Covid-19 pandemic and ahead. CONCLUSION The ongoing development in AI and ML has significantly improved treatment, medication, screening, prediction, forecasting, contact tracing, and drug/vaccine development process for the Covid-19 pandemic and reduce the human intervention in medical practice. However, most of the models are not deployed enough to show their real-world operation, but they are still up to the mark to tackle the SARS-CoV-2 epidemic.
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Affiliation(s)
- Samuel Lalmuanawma
- Department of Mathematics & Computer Science, Mizoram University, Tanhril, Aizawl, Mizoram, 796004, India
| | - Jamal Hussain
- Department of Mathematics & Computer Science, Mizoram University, Tanhril, Aizawl, Mizoram, 796004, India
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Yadav A, Seth B, Chaturvedi RK. Brain Organoids: Tiny Mirrors of Human Neurodevelopment and Neurological Disorders. Neuroscientist 2020; 27:388-426. [PMID: 32723210 DOI: 10.1177/1073858420943192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Unravelling the complexity of the human brain is a challenging task. Nowadays, modern neurobiologists have developed 3D model systems called "brain organoids" to overcome the technical challenges in understanding human brain development and the limitations of animal models to study neurological diseases. Certainly like most model systems in neuroscience, brain organoids too have limitations, as these minuscule brains lack the complex neuronal circuitry required to begin the operational tasks of human brain. However, researchers are hopeful that future endeavors with these 3D brain tissues could provide mechanistic insights into the generation of circuit complexity as well as reproducible creation of different regions of the human brain. Herein, we have presented the contemporary state of brain organoids with special emphasis on their mode of generation and their utility in modelling neurological disorders, drug discovery, and clinical trials.
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Affiliation(s)
- Anuradha Yadav
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Brashket Seth
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajnish Kumar Chaturvedi
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Mietchen D, Li J. Quantifying the Impact of Data Sharing on Outbreak Dynamics (QIDSOD). RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e54770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In this project, we will explore the range of data-related decisions made during public health emergencies like the ongoing COVID-19 pandemic and analyze the flow of information, data, and metadata within networks of such decisions.
Data sharing is now considered a key component of addressing present, future, and even past public health emergencies, from local to global levels. Researchers, research institutions, journals and others have taken steps towards increasing the sharing of data around the ongoing COVID-19 pandemic and in preparation for future pandemics.
We will quantify the effects of data flow modifications to identify parameter sets under which specific modes of sharing or withholding information have the largest effects on outbreak dynamics. For these high-impact parameter sets, we will then assess the current and past availability of corresponding data, metadata, and misinformation, and estimate the effects on outbreak mitigation and preparedness efforts.
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10
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Ekins S, Mottin M, Ramos PRPS, Sousa BKP, Neves BJ, Foil DH, Zorn KM, Braga RC, Coffee M, Southan C, Puhl AC, Andrade CH. Déjà vu: Stimulating open drug discovery for SARS-CoV-2. Drug Discov Today 2020; 25:928-941. [PMID: 32320852 PMCID: PMC7167229 DOI: 10.1016/j.drudis.2020.03.019] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022]
Abstract
In the past decade we have seen two major Ebola virus outbreaks in Africa, the Zika virus in Brazil and the Americas and the current pandemic of coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There is a strong sense of déjà vu because there are still no effective treatments. In the COVID-19 pandemic, despite being a new virus, there are already drugs suggested as active in in vitro assays that are being repurposed in clinical trials. Promising SARS-CoV-2 viral targets and computational approaches are described and discussed. Here, we propose, based on open antiviral drug discovery approaches for previous outbreaks, that there could still be gaps in our approach to drug discovery.
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Affiliation(s)
- Sean Ekins
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA.
| | - Melina Mottin
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO 74605-170, Brazil
| | - Paulo R P S Ramos
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO 74605-170, Brazil
| | - Bruna K P Sousa
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO 74605-170, Brazil
| | - Bruno Junior Neves
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO 74605-170, Brazil
| | - Daniel H Foil
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | | | - Megan Coffee
- Division of Infectious Diseases and Immunology, Department of Medicine, New York University, NY, USA; Department of Population and Family Health, Mailman School of Public Health, Columbia University, NY, USA
| | | | - Ana C Puhl
- Collaborations Pharmaceuticals, 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Carolina Horta Andrade
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO 74605-170, Brazil; Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, SP 13083-864, Brazil.
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11
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Davidson RB, Hendrix J, Geiss BJ, McCullagh M. RNA-Dependent Structures of the RNA-Binding Loop in the Flavivirus NS3 Helicase. J Phys Chem B 2020; 124:2371-2381. [PMID: 32105483 DOI: 10.1021/acs.jpcb.0c00457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The flavivirus NS3 protein is a helicase that has pivotal functions during the viral genome replication process, where it unwinds double-stranded RNA and translocates along the nucleic acid polymer in a nucleoside triphosphate hydrolysis-dependent mechanism. Crystallographic and computational studies of the flavivirus NS3 helicase have identified the RNA-binding loop as an interesting structural element that may function as a component of the RNA-enhanced NTPase activity observed for this family of helicases. Microsecond-long unbiased molecular dynamics and extensive replica exchange umbrella sampling simulations of the Zika NS3 helicase have been performed to investigate the RNA dependence of this loop's structural conformations. Specifically, the effect of the bound single-stranded RNA (ssRNA) oligomer on the putative "open" and "closed" conformations of this loop is studied. In the Apo substrate state, the two loop conformations are nearly isoergonic (ΔAO→C = -0.22 kcal mol-1), explaining the structural ambiguity observed in Apo NS3h crystal structures. The bound ssRNA is seen to stabilize the "open" conformation (ΔAO→C = 1.97 kcal mol-1) through direct protein-RNA interactions at the top of the loop. Interestingly, a small ssRNA oligomer bound over 13 Å away from the loop is seen to affect the free energy surface to favor the "open" structure, while minimizing barriers between the two states. Both the mechanism of the "open" to "closed" transition and important residues of the RNA-binding loop structures are characterized. From these results, point mutations that are hypothesized to stabilize the "closed" RNA-binding loop and negatively impact RNA-binding and the RNA-enhanced NTPase activity are posited.
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Affiliation(s)
- Russell B Davidson
- Department of Chemistry, Colorado State University, Fort Collins 80523, Colorado, United States
| | - Josie Hendrix
- Department of Chemistry, Colorado State University, Fort Collins 80523, Colorado, United States
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins 80523, Colorado, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins 80523, Colorado, United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74074, United States
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12
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Kazmi SS, Ali W, Bibi N, Nouroz F. A review on Zika virus outbreak, epidemiology, transmission and infection dynamics. ACTA ACUST UNITED AC 2020; 27:5. [PMID: 32158705 PMCID: PMC7057477 DOI: 10.1186/s40709-020-00115-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
Zika virus (ZIKV) is a newly emergent relative of the Flaviviridae family and linked to dengue (DENV) and Chikungunya (CHIVKV). ZIKV is one of the rising pathogens promptly surpassing geographical borders. ZIKV infection was characterized by mild disease with fever, headache, rash, arthralgia and conjunctivitis, with exceptional reports of an association with Guillain–Barre syndrome (GBS) and microcephaly. However, since the end of 2015, an increase in the number of GBS associated cases and an astonishing number of microcephaly in fetus and new-borns in Brazil have been related to ZIKV infection, raising serious worldwide public health concerns. ZIKV is transmitted by the bite of infected female mosquitoes of Aedes species. Clarifying such worrisome relationships is, thus, a current unavoidable goal. Here, we extensively described the current understanding of the effects of ZIKV on heath, clinical manifestation, diagnosis and treatment options based on modern, alternative and complementary medicines regarding the disease.
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Affiliation(s)
- Syeda Sidra Kazmi
- 1Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Waqar Ali
- 1Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Nousheen Bibi
- 1Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Faisal Nouroz
- 1Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan.,2Department of Botany, Hazara University Mansehra, Mansehra, Pakistan
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13
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Wang L, Liang R, Gao Y, Li Y, Deng X, Xiang R, Zhang Y, Ying T, Jiang S, Yu F. Development of Small-Molecule Inhibitors Against Zika Virus Infection. Front Microbiol 2019; 10:2725. [PMID: 31866959 PMCID: PMC6909824 DOI: 10.3389/fmicb.2019.02725] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
In recent years, the outbreak of infectious disease caused by Zika virus (ZIKV) has posed a major threat to global public health, calling for the development of therapeutics to treat ZIKV disease. Here, we have described the different stages of the ZIKV life cycle and summarized the latest progress in the development of small-molecule inhibitors against ZIKV infection. We have also discussed some general strategies for the discovery of small-molecule ZIKV inhibitors.
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Affiliation(s)
- Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yaning Gao
- Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yanbai Li
- College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Rong Xiang
- College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yina Zhang
- College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shibo Jiang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Yu
- College of Life and Science, Hebei Agricultural University, Baoding, China
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14
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Kumar D, Aarthy M, Kumar P, Singh SK, Uversky VN, Giri R. Targeting the NTPase site of Zika virus NS3 helicase for inhibitor discovery. J Biomol Struct Dyn 2019; 38:4827-4837. [DOI: 10.1080/07391102.2019.1689851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Deepak Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Murali Aarthy
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University, Karaikudi, Tamilnadu
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University, Karaikudi, Tamilnadu
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Moscow, Russia
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
- BioX Centre, Indian Institute of Technology Mandi, Mandi, India
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15
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Surnar B, Kamran MZ, Shah AS, Basu U, Kolishetti N, Deo S, Jayaweera DT, Daunert S, Dhar S. Orally Administrable Therapeutic Synthetic Nanoparticle for Zika Virus. ACS NANO 2019. [PMID: 31603314 DOI: 10.1021/acsnano.9b0280710.1021/acsnano.9b02807.s001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The spread of Zika virus (ZIKV) infection across the USA and various countries in the last three years will not only have a direct impact on the U.S. health care system but has caused international concerns as well. The ultimate impact of ZIKV infection remains to be understood. Currently, there are no therapeutic or vaccine options available to protect those infected by ZIKV. The drug ivermectin (IVM) was found to be a viable agent for the prevention of transmission of ZIKV. Ivermectin is unstable in the presence of water and does not remain in adequate concentration in the human bloodstream to be effective in treatment for ZIKV. Biodegradable nanoparticles would aid in the delivery of ivermectin by providing a high enough concentration of drug and ensuring the drug is gradually released to maintain an appropriate level in the body. The overall goal of this study was to develop and optimize an orally administrable nanoformulation of IVM which can circulate in the blood for a long period for efficient delivery. To achieve the goal, we synthesized and optimized a synthetic nanoformulation of IVM for oral use which can cross the intestinal epithelial barrier to enter the bloodstream. Our studies documented that when delivered with the synthetic nanoparticle (NP), IVM can be accumulated in the blood at a higher concentration and preliminary studies highlighted that NP delivered IVM has the ability to target nonstructural 1 protein of ZIKV. For potential clinical relevance, long-term storable formulation of IVM-nanoparticle in dry powder state for inclusion in a capsule form and cryoprotectant containing frozen forms revealed promising findings. Further, our preliminary in vitro studies documented that ivermectin crosses the placental barrier, thus making it unsafe for the pregnant ZIKV population, whereas the ivermectin-loaded nanoparticle did not show any significant placental barrier crossing, thus indicating its potential suitability for such population. We envision that this work will fill a great unmet need by developing safer and more effective therapies for the treatment of viral infections, including ZIKV.
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Affiliation(s)
- Bapurao Surnar
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine , University of Miami , 1951 NW 7th Avenue, Suite 475 , Miami , Florida 33136 , United States
| | - Mohammad Z Kamran
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine , University of Miami , 1951 NW 7th Avenue, Suite 475 , Miami , Florida 33136 , United States
| | - Anuj S Shah
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
| | - Uttara Basu
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
| | - Nagesh Kolishetti
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine , Florida International University , Miami , Florida 33199 , United States
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
- Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine , University of Miami , 1475 NW 12th Avenue , Miami , Florida 33136 , United States
| | - Dushyantha T Jayaweera
- University of Miami Clinical and Translational Science Institute, Leonard M. Miller School of Medicine , University of Miami , 1120 NW 14th Street, Suite 710 , Miami , Florida 33136 , United States
- Department of Medicine, Miami Center for AIDS Research, Leonard M. Miller School of Medicine , University of Miami , 1580 NW 10th Avenue , Miami , Florida 33136 , United States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine , University of Miami , 1951 NW 7th Avenue, Suite 475 , Miami , Florida 33136 , United States
- Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine , University of Miami , 1475 NW 12th Avenue , Miami , Florida 33136 , United States
- University of Miami Clinical and Translational Science Institute, Leonard M. Miller School of Medicine , University of Miami , 1120 NW 14th Street, Suite 710 , Miami , Florida 33136 , United States
| | - Shanta Dhar
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine , University of Miami , 1011 NW 15th Street , Miami , Florida 33136 , United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine , University of Miami , 1951 NW 7th Avenue, Suite 475 , Miami , Florida 33136 , United States
- Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine , University of Miami , 1475 NW 12th Avenue , Miami , Florida 33136 , United States
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16
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Evasion of Innate and Intrinsic Antiviral Pathways by the Zika Virus. Viruses 2019; 11:v11100970. [PMID: 31652496 PMCID: PMC6833475 DOI: 10.3390/v11100970] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/19/2019] [Accepted: 10/20/2019] [Indexed: 12/15/2022] Open
Abstract
The Zika virus (ZIKV) is a recently emerged mosquito-borne flavivirus that, while typically asymptomatic, can cause neurological symptoms in adults and birth defects in babies born to infected mothers. The interactions of ZIKV with many different pathways in the human host ultimately determine successful virus replication and ZIKV-induced pathogenesis; however, the molecular mechanisms of such host-ZIKV interactions have just begun to be elucidated. Here, we summarize the recent advances that defined the mechanisms by which ZIKV antagonizes antiviral innate immune signaling pathways, with a particular focus on evasion of the type I interferon response in the human host. Furthermore, we describe emerging evidence that indicated the contribution of several cell-intrinsic mechanisms to an effective restriction of ZIKV infection, such as nonsense-mediated mRNA decay, stress granule formation, and "reticulophagy", a type of selective autophagy. Finally, we summarize the recent work that identified strategies by which ZIKV modulated these intrinsic antiviral responses.
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17
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Surnar B, Kamran MZ, Shah AS, Basu U, Kolishetti N, Deo S, Jayaweera DT, Daunert S, Dhar S. Orally Administrable Therapeutic Synthetic Nanoparticle for Zika Virus. ACS NANO 2019; 13:11034-11048. [PMID: 31603314 PMCID: PMC7053157 DOI: 10.1021/acsnano.9b02807] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The spread of Zika virus (ZIKV) infection across the USA and various countries in the last three years will not only have a direct impact on the U.S. health care system but has caused international concerns as well. The ultimate impact of ZIKV infection remains to be understood. Currently, there are no therapeutic or vaccine options available to protect those infected by ZIKV. The drug ivermectin (IVM) was found to be a viable agent for the prevention of transmission of ZIKV. Ivermectin is unstable in the presence of water and does not remain in adequate concentration in the human bloodstream to be effective in treatment for ZIKV. Biodegradable nanoparticles would aid in the delivery of ivermectin by providing a high enough concentration of drug and ensuring the drug is gradually released to maintain an appropriate level in the body. The overall goal of this study was to develop and optimize an orally administrable nanoformulation of IVM which can circulate in the blood for a long period for efficient delivery. To achieve the goal, we synthesized and optimized a synthetic nanoformulation of IVM for oral use which can cross the intestinal epithelial barrier to enter the bloodstream. Our studies documented that when delivered with the synthetic nanoparticle (NP), IVM can be accumulated in the blood at a higher concentration and preliminary studies highlighted that NP delivered IVM has the ability to target nonstructural 1 protein of ZIKV. For potential clinical relevance, long-term storable formulation of IVM-nanoparticle in dry powder state for inclusion in a capsule form and cryoprotectant containing frozen forms revealed promising findings. Further, our preliminary in vitro studies documented that ivermectin crosses the placental barrier, thus making it unsafe for the pregnant ZIKV population, whereas the ivermectin-loaded nanoparticle did not show any significant placental barrier crossing, thus indicating its potential suitability for such population. We envision that this work will fill a great unmet need by developing safer and more effective therapies for the treatment of viral infections, including ZIKV.
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Affiliation(s)
- Bapurao Surnar
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine, University of Miami, 1951 NW 7th Avenue, Suite 475, Miami, Florida 33136, United States
| | - Mohammad Z. Kamran
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine, University of Miami, 1951 NW 7th Avenue, Suite 475, Miami, Florida 33136, United States
| | - Anuj S. Shah
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
| | - Uttara Basu
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
| | - Nagesh Kolishetti
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
- Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine, University of Miami, 1475 NW 12th Avenue, Miami, Florida 33136, United States
| | - Dushyantha T. Jayaweera
- University of Miami Clinical and Translational Science Institute, Leonard M. Miller School of Medicine, University of Miami, 1120 NW 14th Street, Suite 710, Miami, Florida 33136, United States
- Department of Medicine, Miami Center for AIDS Research, Leonard M. Miller School of Medicine, University of Miami, 1580 NW 10th Avenue, Miami, Florida 33136, United States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine, University of Miami, 1951 NW 7th Avenue, Suite 475, Miami, Florida 33136, United States
- Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine, University of Miami, 1475 NW 12th Avenue, Miami, Florida 33136, United States
- University of Miami Clinical and Translational Science Institute, Leonard M. Miller School of Medicine, University of Miami, 1120 NW 14th Street, Suite 710, Miami, Florida 33136, United States
| | - Shanta Dhar
- Department of Biochemistry and Molecular Biology, Leonard M. Miller School of Medicine, University of Miami, 1011 NW 15th Street, Miami, Florida 33136, United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Leonard M. Miller School of Medicine, University of Miami, 1951 NW 7th Avenue, Suite 475, Miami, Florida 33136, United States
- Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine, University of Miami, 1475 NW 12th Avenue, Miami, Florida 33136, United States
- Corresponding Author:
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18
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Basak SC, Majumdar S, Nandy A, Roy P, Dutta T, Vracko M, Bhattacharjee AK. Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus. Pharmaceuticals (Basel) 2019; 12:E157. [PMID: 31623241 PMCID: PMC6958466 DOI: 10.3390/ph12040157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.
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Affiliation(s)
- Subhash C Basak
- Department of Chemistry and Biochemistry, University of Minnesota, Duluth, MN 55812, USA.
| | | | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Proyasha Roy
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Tathagata Dutta
- Centre for Interdisciplinary Research and Education, Kolkata 700068, India.
| | - Marjan Vracko
- National Institute of Chemistry, Hajdrihova 19, Ljubljana 1000, Slovenia.
| | - Apurba K Bhattacharjee
- Biomedical Graduate Research Organization, Department of Microbiology and Immunology School of Medicine, Georgetown University, Washington, DC 20057, USA.
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19
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Kumar A, Liang B, Aarthy M, Singh SK, Garg N, Mysorekar IU, Giri R. Hydroxychloroquine Inhibits Zika Virus NS2B-NS3 Protease. ACS OMEGA 2018; 3:18132-18141. [PMID: 30613818 PMCID: PMC6312647 DOI: 10.1021/acsomega.8b01002] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/05/2018] [Indexed: 05/30/2023]
Abstract
Zika virus is a mosquito-transmitted flavivirus that causes devastating fetal outcomes in the context of maternal infection during pregnancy. An important target for drugs combatting Zika virus pathogenicity is NS2B-NS3 protease, which plays an essential role in hydrolysis and maturation of the flavivirus polyprotein. We identify hydroxychloroquine, a drug that already has approved uses in pregnancy, as a possible inhibitor of NS2B-NS3 protease by using a Food and Drug Administration-approved drug library, molecular docking, and molecular dynamics simulations. Further, to gain insight into its inhibitory potential toward NS2B-NS3 protease, we performed enzyme kinetic studies, which revealed that hydroxychloroquine inhibits protease activity with an inhibition constant (K i) of 92.34 ± 11.91 μM. Additionally, hydroxychloroquine significantly decreases Zika virus infection in placental cells.
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Affiliation(s)
- Ankur Kumar
- Indian
Institute of Technology Mandi, Mandi 175005, Himachal Pradesh, India
| | - Brooke Liang
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, and Department of
Pathology and Immunology, Washington University
School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, United
States
| | - Murali Aarthy
- Department
of Bioinformatics, Computer Aided Drug Design and Molecular Modeling
Laboratory, Alagappa University, Science Block, Karaikudi 630003, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Department
of Bioinformatics, Computer Aided Drug Design and Molecular Modeling
Laboratory, Alagappa University, Science Block, Karaikudi 630003, Tamil Nadu, India
| | - Neha Garg
- Indian
Institute of Technology Mandi, Mandi 175005, Himachal Pradesh, India
- BioX Center, Indian Institute
of Technology Mandi, Mandi 175005, Himachal Pradesh, India
| | - Indira U. Mysorekar
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, and Department of
Pathology and Immunology, Washington University
School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, United
States
| | - Rajanish Giri
- Indian
Institute of Technology Mandi, Mandi 175005, Himachal Pradesh, India
- BioX Center, Indian Institute
of Technology Mandi, Mandi 175005, Himachal Pradesh, India
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20
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Hernandez HW, Soeung M, Zorn KM, Ashoura N, Mottin M, Andrade CH, Caffrey CR, de Siqueira-Neto JL, Ekins S. High Throughput and Computational Repurposing for Neglected Diseases. Pharm Res 2018; 36:27. [PMID: 30560386 PMCID: PMC6792295 DOI: 10.1007/s11095-018-2558-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/09/2018] [Indexed: 12/21/2022]
Abstract
Purpose Neglected tropical diseases (NTDs) represent are a heterogeneous group of communicable diseases that are found within the poorest populations of the world. There are 23 NTDs that have been prioritized by the World Health Organization, which are endemic in 149 countries and affect more than 1.4 billion people, costing these developing economies billions of dollars annually. The NTDs result from four different causative pathogens: protozoa, bacteria, helminth and virus. The majority of the diseases lack effective treatments. Therefore, new therapeutics for NTDs are desperately needed. Methods We describe various high throughput screening and computational approaches that have been performed in recent years. We have collated the molecules identified in these studies and calculated molecular properties. Results Numerous global repurposing efforts have yielded some promising compounds for various neglected tropical diseases. These compounds when analyzed as one would expect appear drug-like. Several large datasets are also now in the public domain and this enables machine learning models to be constructed that then facilitate the discovery of new molecules for these pathogens. Conclusions In the space of a few years many groups have either performed experimental or computational repurposing high throughput screens against neglected diseases. These have identified compounds which in many cases are already approved drugs. Such approaches perhaps offer a more efficient way to develop treatments which are generally not a focus for global pharmaceutical companies because of the economics or the lack of a viable market. Other diseases could perhaps benefit from these repurposing approaches. Electronic supplementary material The online version of this article (10.1007/s11095-018-2558-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Melinda Soeung
- MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina, 27606, USA
| | | | - Melina Mottin
- LabMol - Laboratory for Molecular Modeling and Drug Design Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO, 74605-170, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO, 74605-170, Brazil
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, 92093, USA
| | - Jair Lage de Siqueira-Neto
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, 92093, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina, 27606, USA.
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21
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Mottin M, Borba JVVB, Melo-Filho CC, Neves BJ, Muratov E, Torres PHM, Braga RC, Perryman A, Ekins S, Andrade CH. Computational drug discovery for the Zika virus. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000001002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
| | | | | | - Bruno Junior Neves
- Federal University of Goiás, Brazil; University Center of Anápolis, Brazil
| | - Eugene Muratov
- University of North Carolin, USA; Odessa National Polytechnic University, Ukraine
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22
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Sinigaglia A, Riccetti S, Trevisan M, Barzon L. In silico approaches to Zika virus drug discovery. Expert Opin Drug Discov 2018; 13:825-835. [PMID: 30160181 DOI: 10.1080/17460441.2018.1515909] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION After the WHO declared Zika virus (ZIKV) as a public health emergency of international concern, intense research for the development of vaccines and drugs has been undertaken, leading to the development of several candidates. Areas covered: This review discusses the developments achieved so far by computational methods in the discovery of candidate compounds targeting ZIKV proteins, i.e. the envelope and capsid structural proteins, the NS3 helicase/protease, and the NS5 methyltransferase/RNA-dependent RNA polymerase. Expert opinion: Research for effective drugs against ZIKV is still in a very early discovery phase. Notwithstanding the intense efforts for the development of new drugs and the identification of several promising candidates by using different approaches, including computational methods, so far only a few candidates have been experimentally tested. An important caveat of anti-flavivirus drug development is represented by the difficult of reproducing the in vivo microenvironment of the replication complex, which may lead to discrepancies between in vitro results and experimental evaluation in vivo. Moreover, anti-ZIKV drugs have the additional requirement of an excellent safety profile in pregnancy and ability to diffuse to different tissues, including the central nervous system, the testis, and the placenta.
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Affiliation(s)
| | - Silvia Riccetti
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Marta Trevisan
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Luisa Barzon
- a Department of Molecular Medicine , University of Padova , Padova , Italy
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23
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Routhu NK, Xie Y, Dunworth M, Casero RA, Oupicky D, Byrareddy SN. Polymeric Prodrugs Targeting Polyamine Metabolism Inhibit Zika Virus Replication. Mol Pharm 2018; 15:4284-4295. [PMID: 30040423 DOI: 10.1021/acs.molpharmaceut.8b00068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Zika virus (ZIKV) is primarily transmitted via an infected mosquito bite, during sexual intercourse, or in utero mother to child transmission. When a fetus is infected, both neurological malformations and deficits in brain development are frequently manifested. As such, there is a need for vaccines or drugs that may be used to cure ZIKV infections. Metabolic pathways play a crucial role in cell differentiation and development. More importantly, polyamines play a key role in replication and translation of several RNA viruses, including ZIKV, Dengue virus, and Chikungunya virus. Here, we present polyamine analogues (BENSpm and PG11047) and their corresponding polymer prodrug derivatives for inhibiting ZIKV infection by intersecting with polyamine catabolism pathways. We tested the compounds against ZIKV African (MR766) and Asian (PRVABC59) strains in human kidney epithelial (Vero) and glioblastoma derived (SNB-19) cell lines. Our results demonstrate potent inhibition of ZIKV viral replication in both cell lines tested. This antiviral effect was mediated by the upregulation of two polyamine catabolic enzymes, spermine oxidase, and spermidine (SMOX)/spermine N1-acetyltransferase (SAT1) as apparent reduction of the ZIKV infection following heterologous expression of SMOX and SAT1. On the basis of these observations, we infer potential use of these polyamine analogues to treat ZIKV infections.
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Affiliation(s)
- Nanda Kishore Routhu
- Department of Pharmacology and Experimental Neuroscience , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States
| | - Ying Xie
- Center for Drug Delivery and Nanomedicine Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States
| | - Matthew Dunworth
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Robert A Casero
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - David Oupicky
- Center for Drug Delivery and Nanomedicine Department of Pharmaceutical Sciences , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience , University of Nebraska Medical Center , Omaha , Nebraska 68198 , United States
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24
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Mottin M, Borba JVVB, Braga RC, Torres PHM, Martini MC, Proenca-Modena JL, Judice CC, Costa FTM, Ekins S, Perryman AL, Horta Andrade C. The A-Z of Zika drug discovery. Drug Discov Today 2018; 23:1833-1847. [PMID: 29935345 PMCID: PMC7108251 DOI: 10.1016/j.drudis.2018.06.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/23/2018] [Accepted: 06/14/2018] [Indexed: 02/07/2023]
Abstract
Despite the recent outbreak of Zika virus (ZIKV), there are still no approved treatments, and early-stage compounds are probably many years away from approval. A comprehensive A-Z review of the recent advances in ZIKV drug discovery efforts is presented, highlighting drug repositioning and computationally guided compounds, including discovered viral and host cell inhibitors. Promising ZIKV molecular targets are also described and discussed, as well as targets belonging to the host cell, as new opportunities for ZIKV drug discovery. All this knowledge is not only crucial to advancing the fight against the Zika virus and other flaviviruses but also helps us prepare for the next emerging virus outbreak to which we will have to respond.
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Affiliation(s)
- Melina Mottin
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO 74605-170, Brazil
| | - Joyce V V B Borba
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO 74605-170, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO 74605-170, Brazil
| | - Pedro H M Torres
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ 21040-900, Brazil; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Matheus C Martini
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, SP 13083-864, Brazil
| | - Jose Luiz Proenca-Modena
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, SP 13083-864, Brazil
| | - Carla C Judice
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, SP 13083-864, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, SP 13083-864, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Alexander L Perryman
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ 07103, USA
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO 74605-170, Brazil; Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, SP 13083-864, Brazil.
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25
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Sarukhanyan E, Shityakov S, Dandekar T. In Silico Designed Axl Receptor Blocking Drug Candidates Against Zika Virus Infection. ACS OMEGA 2018; 3:5281-5290. [PMID: 30023915 PMCID: PMC6044927 DOI: 10.1021/acsomega.8b00223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/13/2018] [Indexed: 05/24/2023]
Abstract
After a large outbreak in Brazil, novel drugs against Zika virus became extremely necessary. Evaluation of virus-based pharmacological strategies concerning essential host factors brought us to the idea that targeting the Axl receptor by blocking its dimerization function could be critical for virus entry. Starting from experimentally validated compounds, such as RU-301, RU-302, warfarin, and R428, we identified a novel compound 2' (R428 derivative) to be the most potent for this task amongst a number of alternative compounds and leads. The improved affinity of compound 2' was confirmed by molecular docking as well as molecular dynamics simulation techniques using implicit solvation models. The current study summarizes a new possibility for inhibition of the Axl function as a potential target for future antiviral therapies.
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Affiliation(s)
- Edita Sarukhanyan
- Department
of Bioinformatics, Biocenter, University
of Würzburg, Am
Hubland, 97074 Würzburg, Germany
| | - Sergey Shityakov
- Department
of Anesthesia and Critical Care, University
Hospital Würzburg, Oberdürrbacher Str. 6, 97080 Würzburg, Germany
| | - Thomas Dandekar
- Department
of Bioinformatics, Biocenter, University
of Würzburg, Am
Hubland, 97074 Würzburg, Germany
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26
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Panwar U, Singh SK. An Overview on Zika Virus and the Importance of Computational Drug Discovery. JOURNAL OF EXPLORATORY RESEARCH IN PHARMACOLOGY 2018; 3:43-51. [DOI: 10.14218/jerp.2017.00025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Usman S, Naz Z, Saleem K, Bashir H, Bilal M, Sumrin A. The countermeasure for Zika virus: a hard nut to be cracked. Future Virol 2018. [DOI: 10.2217/fvl-2018-0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The emergence of Zika virus (ZIKV) infection in America has caused a new threat worldwide, as it is linked with the increased incidence of congenital microcephaly in neonates and development of Guillain–Barré syndrome. A number of potential antiviral drugs such as sofosbuvir, BCX4430, NITD008 and 7-DMA have shown activity against ZIKV both in vitro and in vivo. Similarly, different research organizations and academic institutions are trying hard to develop a vaccine against the ZIKV. Some of these groups have received approval from the US FDA to start Phase I clinical trials. Immuno-based treatment strategies, such as use of humanized monoclonal antibodies (hE16 and CR4373) have also entered clinical trials. However, a licensed vaccine is still a long way off and efforts should be made to accelerate the evaluation procedures while minimizing the delay in licensing.
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Affiliation(s)
- Sana Usman
- Center for Applied Molecular Biology, 87-West Canal, Bank Road, University of the Punjab, Lahore-53700, Pakistan
| | - Zara Naz
- Center for Applied Molecular Biology, 87-West Canal, Bank Road, University of the Punjab, Lahore-53700, Pakistan
| | - Komal Saleem
- Center for Applied Molecular Biology, 87-West Canal, Bank Road, University of the Punjab, Lahore-53700, Pakistan
| | - Hamid Bashir
- Center for Applied Molecular Biology, 87-West Canal, Bank Road, University of the Punjab, Lahore-53700, Pakistan
| | - Muhammad Bilal
- Center for Applied Molecular Biology, 87-West Canal, Bank Road, University of the Punjab, Lahore-53700, Pakistan
| | - Aleena Sumrin
- Center for Applied Molecular Biology, 87-West Canal, Bank Road, University of the Punjab, Lahore-53700, Pakistan
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28
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Han Y, Mesplède T, Xu H, Quan Y, Wainberg MA. The antimalarial drug amodiaquine possesses anti-ZIKA virus activities. J Med Virol 2018; 90:796-802. [PMID: 29315671 DOI: 10.1002/jmv.25031] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/24/2017] [Indexed: 02/02/2023]
Abstract
Zika virus (ZIKV) outbreak has emerged as a global health threat, particularly in tropical areas, over the past few years. No antiviral therapy or vaccine is available at present. For these reasons, repurposing clinically approved drugs against ZIKV infection may provide rapid and cost-effective global health benefits. Here, we explored this strategy and screened eight FDA-approved drugs for antiviral activity against ZIKV using a cell-based assay. Our results show that the antimalarial drug amodiaquine has anti-ZIKV activity with EC50 at low micromolar concentrations in cell culture. We further characterized amodiaquine antiviral activity against ZIKV and found that it targets early events of the viral replication cycle. Altogether, our results suggest that amodiaquine may be efficacious for the treatment of ZIKV infection.
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Affiliation(s)
- Yingshan Han
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Thibault Mesplède
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Faculty of Medicine, Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Hongtao Xu
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yudong Quan
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Faculty of Medicine, Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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29
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Mittal R, Nguyen D, Debs LH, Patel AP, Liu G, Jhaveri VM, S. Kay SI, Mittal J, Bandstra ES, Younis RT, Chapagain P, Jayaweera DT, Liu XZ. Zika Virus: An Emerging Global Health Threat. Front Cell Infect Microbiol 2017; 7:486. [PMID: 29276699 PMCID: PMC5727043 DOI: 10.3389/fcimb.2017.00486] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/13/2017] [Indexed: 01/07/2023] Open
Abstract
Zika virus (ZIKV) is an emerging healthcare threat. The presence of the mosquito Aedes species across South and Central America in combination with complementary climates have incited an epidemic of locally transmitted cases of ZIKV infection in Brazil. As one of the most significant current public health concerns in the Americas, ZIKV epidemic has been a cause of alarm due to its known and unknown complications. At this point, there has been a clear association between ZIKV infection and severe clinical manifestations in both adults and neonates, including but not limited to neurological deficits such as Guillain-Barré syndrome (GBS) and microcephaly, respectively. The gravity of the fetal anomalies linked to ZIKV vertical transmission from the mother has prompted a discussion on whether to include ZIKV as a formal member of the TORCH [Toxoplasma gondii, other, rubella virus, cytomegalovirus (CMV), and herpes] family of pathogens known to breach placental barriers and cause congenital disease in the fetus. The mechanisms of these complex phenotypes have yet to be fully described. As such, diagnostic tools are limited and no effective modalities are available to treat ZIKV. This article will review the recent advancements in understanding the pathogenesis of ZIKV infection as well as diagnostic tests available to detect the infection. Due to the increase in incidence of ZIKV infections, there is an immediate need to develop new diagnostic tools and novel preventive as well as therapeutic modalities based on understanding the molecular mechanisms underlying the disease.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States,*Correspondence: Rahul Mittal
| | - Desiree Nguyen
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Luca H. Debs
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Amit P. Patel
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - George Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Vasanti M. Jhaveri
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sae-In S. Kay
- Department of Surgery, Division of Otorhinolaryngology, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jeenu Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Emmalee S. Bandstra
- Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ramzi T. Younis
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States,Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, FL, United States
| | - Dushyantha T. Jayaweera
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, United States,Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States,Xue Zhong Liu
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30
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Shankar A, Patil AA, Skariyachan S. Recent Perspectives on Genome, Transmission, Clinical Manifestation, Diagnosis, Therapeutic Strategies, Vaccine Developments, and Challenges of Zika Virus Research. Front Microbiol 2017; 8:1761. [PMID: 28959246 PMCID: PMC5603822 DOI: 10.3389/fmicb.2017.01761] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/30/2017] [Indexed: 12/13/2022] Open
Abstract
One of the potential threats to public health microbiology in 21st century is the increased mortality rate caused by Zika virus (ZIKV), a mosquito-borne flavivirus. The severity of ZIKV infection urged World Health Organization (WHO) to declare this virus as a global concern. The limited knowledge on the structure, virulent factors, and replication mechanism of the virus posed as hindrance for vaccine development. Several vector and non-vector-borne mode of transmission are observed for spreading the disease. The similarities of the virus with other flaviviruses such as dengue and West Nile virus are worrisome; hence, there is high scope to undertake ZIKV research that probably provide insight for novel therapeutic intervention. Thus, this review focuses on the recent aspect of ZIKV research which includes the outbreak, genome structure, multiplication and propagation of the virus, current animal models, clinical manifestations, available treatment options (probable vaccines and therapeutics), and the recent advancements in computational drug discovery pipelines, challenges and limitation to undertake ZIKV research. The review suggests that the infection due to ZIKV became one of the universal concerns and an interdisciplinary environment of in vitro cellular assays, genomics, proteomics, and computational biology approaches probably contribute insights for screening of novel molecular targets for drug design. The review tried to provide cutting edge knowledge in ZIKV research with future insights required for the development of novel therapeutic remedies to curtail ZIKV infection.
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Affiliation(s)
- Apoorva Shankar
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar InstitutionsBengaluru, India
| | - Amulya A Patil
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar InstitutionsBengaluru, India
| | - Sinosh Skariyachan
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar InstitutionsBengaluru, India.,Visvesvaraya Technological UniversityBelagavi, India
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31
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Mumtaz N, Jimmerson LC, Bushman LR, Kiser JJ, Aron G, Reusken CBEM, Koopmans MPG, van Kampen JJA. Cell-line dependent antiviral activity of sofosbuvir against Zika virus. Antiviral Res 2017; 146:161-163. [PMID: 28912011 DOI: 10.1016/j.antiviral.2017.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 07/17/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
The recent epidemic of Zika virus (ZIKV) in the Americas and its association with fetal and neurological complications has shown the need to develop a treatment. Repurposing of drugs that are already FDA approved or in clinical development may shorten drug development timelines in case of emerging viral diseases like ZIKV. Initial studies have shown conflicting results when testing sofosbuvir developed for treatment of infections with another Flaviviridae virus, hepatitis C virus. We hypothesized that the conflicting results could be explained by differences in intracellular processing of the compound. We assessed the antiviral activity of sofosbuvir and mericitabine against ZIKV using Vero, A549, and Huh7 cells and measured the level of the active sofosbuvir metabolite by mass spectrometry. Mericitabine did not show activity, while sofosbuvir inhibited ZIKV with an IC50 of ∼4 μM, but only in Huh7 cells. This correlated with differences in intracellular concentration of the active triphosphate metabolite of sofosbuvir, GS-461203 or 007-TP, which was 11-342 times higher in Huh7 cells compared to Vero and A549 cells. These results show that a careful selection of cell system for repurposing trials of prodrugs is needed for evaluation of antiviral activity. Furthermore, the intracellular levels of 007-TP in tissues and cell types that support ZIKV replication in vivo should be determined to further investigate the potential of sofosbuvir as anti-ZIKV compound.
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Affiliation(s)
- Noreen Mumtaz
- Department of Viroscience, Unit Clinical Virology, Erasmus MC, Rotterdam, The Netherlands
| | - Leah C Jimmerson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, USA
| | - Lane R Bushman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, USA
| | - Jennifer J Kiser
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, USA
| | - Georgina Aron
- Department of Viroscience, Unit Clinical Virology, Erasmus MC, Rotterdam, The Netherlands
| | - Chantal B E M Reusken
- Department of Viroscience, Unit Clinical Virology, Erasmus MC, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Unit Clinical Virology, Erasmus MC, Rotterdam, The Netherlands
| | - Jeroen J A van Kampen
- Department of Viroscience, Unit Clinical Virology, Erasmus MC, Rotterdam, The Netherlands.
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32
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Bajpai VK, Chandra V, Kim NH, Rai R, Kumar P, Kim K, Aeron A, Kang SC, Maheshwari DK, Na M, Rather IA, Park YH. Ghost probiotics with a combined regimen: a novel therapeutic approach against the Zika virus, an emerging world threat. Crit Rev Biotechnol 2017; 38:438-454. [PMID: 28877637 DOI: 10.1080/07388551.2017.1368445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Zika virus (ZIKV) used to be an obscure flavivirus closely related to dengue virus (DENV). Transmission of this epidemic pathogen occurs mainly via mosquitoes, but it is also capable of placental and sexual transmission. Although the characteristics of these viruses are well defined, infections are unpredictable in terms of disease severity, unusual clinical manifestations, unexpected methods of transmission, long-term persistence, and the development of new strains. Recently, ZIKV has gained huge medical attention following the large-scale epidemics around the world, and reported cases of congenital abnormalities associated with Zika virus infections which have created a public health emergency of international concern. Despite continuous research on ZIKV, no specific treatment or vaccine has been developed, excepting a preventive strategy for congenital ZIKV infection. Probiotics, known as GRAS, are bacteria that confer various health beneficial effects, and have been shown to be effective at curing a number of viral diseases by modulating the immune system. Furthermore, probiotic preparations consisting of dead cells and cellular metabolites, so-called "Ghost probiotics", can also act as biological response modifiers. Here, we review available information on the epidemiology, transmission, and clinical features of ZIKV, and on treatment and prevention strategies. In addition, we emphasize the use of probiotics and plant-based natural remedies and describe their action mechanisms, and the green technologies for microbial conversion, which could contribute to the development of novel therapies that may reduce the pathogenicity of ZIKV. Accordingly, we draw attention to new findings, unanswered questions, unresolved issues, and controversies regarding ZIKV.
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Affiliation(s)
- Vivek K Bajpai
- a Department of Applied Microbiology and Biotechnology, School of Biotechnology , Yeungnam University , Gyeongsan , Gyeongbuk , Korea
| | - Vishal Chandra
- b Department of Biosciences , Integral University , Lucknow , India.,c Stephenson Cancer Center (SCC) , University of Oklahoma Health Sciences Center (OUHSC) , Oklahoma City , OK , USA
| | - Na-Hyung Kim
- d Department of Oriental Pharmacy , Wonkwang University , Iksan-city , Jeonbuk , Korea
| | - Rajni Rai
- e School of Biotechnology , Yeungnam University , Gyeongsan , Gyeongbuk , Korea
| | - Pradeep Kumar
- e School of Biotechnology , Yeungnam University , Gyeongsan , Gyeongbuk , Korea
| | - Kangmin Kim
- f Division of Biotechnology, College of Environmental and Bioresource Sciences , Chonbuk National University , Iksan-si , Jeonbuk , Korea
| | - Abhinav Aeron
- f Division of Biotechnology, College of Environmental and Bioresource Sciences , Chonbuk National University , Iksan-si , Jeonbuk , Korea
| | - Sun Chul Kang
- g Department of Biotechnology, College of Engineering , Daegu University , Gyeongsan , Gyeongbuk , Korea
| | - D K Maheshwari
- h Department of Botany and Microbiology , Gurukul Kangri University , Haridwar , India
| | - MinKyun Na
- i College of Pharmacy , Chungnam National University , Daejeon , Korea
| | - Irfan A Rather
- a Department of Applied Microbiology and Biotechnology, School of Biotechnology , Yeungnam University , Gyeongsan , Gyeongbuk , Korea
| | - Yong-Ha Park
- a Department of Applied Microbiology and Biotechnology, School of Biotechnology , Yeungnam University , Gyeongsan , Gyeongbuk , Korea
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33
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Ramharack P, Soliman MES. Zika virus NS5 protein potential inhibitors: an enhanced in silico approach in drug discovery. J Biomol Struct Dyn 2017; 36:1118-1133. [PMID: 28351337 DOI: 10.1080/07391102.2017.1313175] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The re-emerging Zika virus (ZIKV) is an arthropod-borne virus that has been described to have explosive potential as a worldwide pandemic. The initial transmission of the virus was through a mosquito vector, however, evolving modes of transmission has allowed the spread of the disease over continents. The virus has already been linked to irreversible chronic central nervous system conditions. The concerns of the scientific and clinical community are the consequences of Zika viral mutations, thus suggesting the urgent need for viral inhibitors. There have been large strides in vaccine development against the virus but there are still no FDA approved drugs available. Rapid rational drug design and discovery research is fundamental in the production of potent inhibitors against the virus that will not just mask the virus, but destroy it completely. In silico drug design allows for this prompt screening of potential leads, thus decreasing the consumption of precious time and resources. This study demonstrates an optimized and proven screening technique in the discovery of two potential small molecule inhibitors of ZIKV Methyltransferase and RNA dependent RNA polymerase. This in silico 'per-residue energy decomposition pharmacophore' virtual screening approach will be critical in aiding scientists in the discovery of not only effective inhibitors of Zika viral targets, but also a wide range of anti-viral agents.
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Affiliation(s)
- Pritika Ramharack
- a Molecular Modeling and Drug Design Research Group , School of Health Sciences, University of KwaZulu-Natal , Westville Campus, Durban 4001 , South Africa
| | - Mahmoud E S Soliman
- a Molecular Modeling and Drug Design Research Group , School of Health Sciences, University of KwaZulu-Natal , Westville Campus, Durban 4001 , South Africa.,b Pharmaceutical Sciences , University of KwaZulu-Natal , Westville Campus, Durban 4001 , South Africa.,c Faculty of Pharmacy, Department of Pharmaceutical Organic Chemistry , Zagazig University , Zagazig , Egypt.,d College of Pharmacy and Pharmaceutical Sciences, Florida Agricultural and Mechanical University, FAMU , Tallahassee , FL 32307 , USA
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34
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Possas C, Brasil P, Marzochi MC, Tanuri A, Martins RM, Marques ET, Bonaldo MC, Ferreira AG, Lourenço-de-Oliveira R, Nogueira RMR, Sequeira PC, Marzochi KB, Homma A. Zika puzzle in Brazil: peculiar conditions of viral introduction and dissemination - A Review. Mem Inst Oswaldo Cruz 2017; 112:319-327. [PMID: 28443985 PMCID: PMC5398166 DOI: 10.1590/0074-02760160510] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/20/2017] [Indexed: 11/25/2022] Open
Abstract
This article discusses the peculiar conditions that favoured the unexpected introduction of Zika virus into the poorest northeastern region of Brazil in 2015, its speed of transmission to other Brazilian states, other Latin American countries and other regions, and the severity of related neurological disorders in newborns and adults. Contrasting with evidence that Zika had so far caused only mild cases in humans in the last six decades, the epidemiological scenario of this outbreak in Brazil indicates dramatic health effects: in 2015, an increase of 20-fold in notified cases of microcephaly and/or central nervous system (CNS) alterations suggestive of Zika congenital infection, followed by an exponential increase in 2016, with 2366 cumulative cases confirmed in the country by the end of December 2016. A significant increase in Guillain-Barré syndrome in adults has also been reported. Factors involved in viral dissemination, neural pathogenesis and routes of transmission in Brazil are examined, such as the role of social and environmental factors and the controversies involved in the hypothesis of antibody-dependent enhancement, to explain the incidence of congenital Zika syndrome in Brazil. Responses to the Zika outbreak and the development of new products are also discussed.
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Affiliation(s)
- Cristina Possas
- Fundação Oswaldo Cruz-Fiocruz, Bio-Manguinhos, Assessoria Científica Sênior, Rio de Janeiro, RJ, Brasil
| | - Patricia Brasil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Rio de Janeiro, RJ, Brasil
| | - Mauro Ca Marzochi
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses, Rio de Janeiro, RJ, Brasil
| | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Rio de Janeiro, RJ, Brasil
| | - Reinaldo M Martins
- Fundação Oswaldo Cruz-Fiocruz, Bio-Manguinhos, Assessoria Científica Sênior, Rio de Janeiro, RJ, Brasil
| | - Ernesto Ta Marques
- Fundação Oswaldo Cruz-Fiocruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil.,University of Pittsburgh, Center for Vaccine Research, Pittsburgh, PA, United States
| | - Myrna C Bonaldo
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Biologia Molecular de Flavivírus, Rio de Janeiro, RJ, Brasil
| | - Antonio Gp Ferreira
- Fundação Oswaldo Cruz-Fiocruz, Bio-Manguinhos, Departamento de Reativos para Diagnóstico, Rio de Janeiro, RJ, Brasil
| | - Ricardo Lourenço-de-Oliveira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Mosquitos Transmissores de Hematozoários, Rio de Janeiro, RJ, Brasil
| | - Rita Maria R Nogueira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Flavivírus, Rio de Janeiro, RJ, Brasil
| | - Patricia C Sequeira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Flavivírus, Rio de Janeiro, RJ, Brasil
| | - Keyla Bf Marzochi
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica e Vigilância em Leishmanioses, Rio de Janeiro, RJ, Brasil
| | - Akira Homma
- Fundação Oswaldo Cruz-Fiocruz, Bio-Manguinhos, Assessoria Científica Sênior, Rio de Janeiro, RJ, Brasil
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Rausch K, Hackett BA, Weinbren NL, Reeder SM, Sadovsky Y, Hunter CA, Schultz DC, Coyne CB, Cherry S. Screening Bioactives Reveals Nanchangmycin as a Broad Spectrum Antiviral Active against Zika Virus. Cell Rep 2017; 18:804-815. [PMID: 28099856 PMCID: PMC5270376 DOI: 10.1016/j.celrep.2016.12.068] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/07/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022] Open
Abstract
Zika virus is an emerging arthropod-borne flavivirus for which there are no vaccines or specific therapeutics. We screened a library of 2,000 bioactive compounds for their ability to block Zika virus infection in three distinct cell types with two different strains of Zika virus. Using a microscopy-based assay, we validated 38 drugs that inhibited Zika virus infection, including FDA-approved nucleoside analogs. Cells expressing high levels of the attachment factor AXL can be protected from infection with receptor tyrosine kinase inhibitors, while placental-derived cells that lack AXL expression are insensitive to this inhibition. Importantly, we identified nanchangmycin as a potent inhibitor of Zika virus entry across all cell types tested, including physiologically relevant primary cells. Nanchangmycin also was active against other medically relevant viruses, including West Nile, dengue, and chikungunya viruses that use a similar route of entry. This study provides a resource of small molecules to study Zika virus pathogenesis.
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Affiliation(s)
- Keiko Rausch
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brent A Hackett
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathan L Weinbren
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sophia M Reeder
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Obstetrics, Gynecology, and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 19104, USA
| | - Christopher A Hunter
- Department of Pathobiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David C Schultz
- High-Throughput Screening Core, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carolyn B Coyne
- Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Obstetrics, Gynecology, and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 19104, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 19104, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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36
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Zhang Z, Li Y, Loh YR, Phoo WW, Hung AW, Kang C, Luo D. Crystal structure of unlinked NS2B-NS3 protease from Zika virus. Science 2016; 354:1597-1600. [PMID: 27940580 DOI: 10.1126/science.aai9309] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Zika virus (ZIKV) has rapidly emerged as a global public health concern. Viral NS2B-NS3 protease processes viral polyprotein and is essential for the virus replication, making it an attractive antiviral drug target. We report crystal structures at 1.58-angstrom resolution of the unlinked NS2B-NS3 protease from ZIKV as free enzyme and bound to a peptide reversely oriented at the active site. The unlinked NS2B-NS3 protease adopts a closed conformation in which NS2B engages NS3 to form an empty substrate-binding site. A second protease in the same crystal binds to the residues K14K15G16E17 from the neighboring NS3 in reverse orientation, resisting proteolysis. These features of ZIKV NS2B-NS3 protease may accelerate the discovery of structure-based antiviral drugs against ZIKV and related pathogenic flaviviruses.
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Affiliation(s)
- Zhenzhen Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building 06-01, 59 Nanyang Drive, Singapore 636921
| | - Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669
| | - Ying Ru Loh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669
| | - Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building 06-01, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669.
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921. .,NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building 06-01, 59 Nanyang Drive, Singapore 636921
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37
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Ekins S, Liebler J, Neves BJ, Lewis WG, Coffee M, Bienstock R, Southan C, Andrade CH. Illustrating and homology modeling the proteins of the Zika virus. F1000Res 2016; 5:275. [PMID: 27746901 DOI: 10.12688/f1000research.8213.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/28/2022] Open
Abstract
The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, USA; Collaborations Pharmaceuticals Inc., Fuquay-Varina, NC, USA; Collaborative Drug Discovery Inc, Burlingame, CA, USA
| | | | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
| | - Warren G Lewis
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Megan Coffee
- The International Rescue Committee, New York, NY, USA
| | | | | | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
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Abstract
The Zika virus outbreak in the Americas has caused global concern. To help accelerate this fight against Zika, we launched the OpenZika project. OpenZika is an IBM World Community Grid Project that uses distributed computing on millions of computers and Android devices to run docking experiments, in order to dock tens of millions of drug-like compounds against crystal structures and homology models of Zika proteins (and other related flavivirus targets). This will enable the identification of new candidates that can then be tested in vitro, to advance the discovery and development of new antiviral drugs against the Zika virus. The docking data is being made openly accessible so that all members of the global research community can use it to further advance drug discovery studies against Zika and other related flaviviruses.
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39
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Barrows NJ, Campos RK, Powell ST, Prasanth KR, Schott-Lerner G, Soto-Acosta R, Galarza-Muñoz G, McGrath EL, Urrabaz-Garza R, Gao J, Wu P, Menon R, Saade G, Fernandez-Salas I, Rossi SL, Vasilakis N, Routh A, Bradrick SS, Garcia-Blanco MA. A Screen of FDA-Approved Drugs for Inhibitors of Zika Virus Infection. Cell Host Microbe 2016; 20:259-70. [PMID: 27476412 PMCID: PMC4993926 DOI: 10.1016/j.chom.2016.07.004] [Citation(s) in RCA: 364] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/19/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022]
Abstract
Currently there are no approved vaccines or specific therapies to prevent or treat Zika virus (ZIKV) infection. We interrogated a library of FDA-approved drugs for their ability to block infection of human HuH-7 cells by a newly isolated ZIKV strain (ZIKV MEX_I_7). More than 20 out of 774 tested compounds decreased ZIKV infection in our in vitro screening assay. Selected compounds were further validated for inhibition of ZIKV infection in human cervical, placental, and neural stem cell lines, as well as primary human amnion cells. Established anti-flaviviral drugs (e.g., bortezomib and mycophenolic acid) and others that had no previously known antiviral activity (e.g., daptomycin) were identified as inhibitors of ZIKV infection. Several drugs reduced ZIKV infection across multiple cell types. This study identifies drugs that could be tested in clinical studies of ZIKV infection and provides a resource of small molecules to study ZIKV pathogenesis.
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Affiliation(s)
- Nicholas J Barrows
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Rafael K Campos
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Steven T Powell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA
| | - K Reddisiva Prasanth
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA
| | - Geraldine Schott-Lerner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA
| | - Ruben Soto-Acosta
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA
| | - Gaddiel Galarza-Muñoz
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA
| | - Erica L McGrath
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Rheanna Urrabaz-Garza
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Junling Gao
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Ping Wu
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Ramkumar Menon
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - George Saade
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Ildefonso Fernandez-Salas
- Centro Regional de Investigación en Salud Publica INSP, 19 Poniente Esquina 4(a) Norte s/n, Colonia Centro, Tapachula, Chiapas 30700, C.P., Mexico
| | - Shannan L Rossi
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, and Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, and Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA.
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, 301 University Blvd, Galveston, TX 77555, USA; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Republic of Singapore.
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40
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Ekins S, Liebler J, Neves BJ, Lewis WG, Coffee M, Bienstock R, Southan C, Andrade CH. Illustrating and homology modeling the proteins of the Zika virus. F1000Res 2016; 5:275. [PMID: 27746901 PMCID: PMC5040154 DOI: 10.12688/f1000research.8213.2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/30/2016] [Indexed: 12/20/2022] Open
Abstract
The Zika virus (ZIKV) is a flavivirus of the family
Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either
in vitro or
in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, USA; Collaborations Pharmaceuticals Inc., Fuquay-Varina, NC, USA; Collaborative Drug Discovery Inc, Burlingame, CA, USA
| | | | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
| | - Warren G Lewis
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Megan Coffee
- The International Rescue Committee, New York, NY, USA
| | | | | | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, GO, Brazil
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41
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Ramharack P, Soliman MES. Zika virus drug targets: a missing link in drug design and discovery – a route map to fill the gap. RSC Adv 2016. [DOI: 10.1039/c6ra12142j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review depicts anin silicoroute map for ZIKV drug discovery, thus revealing novel potential inhibitors of viral replication.
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Affiliation(s)
- Pritika Ramharack
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahmoud E. S. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
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