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Puhl AC, Lane TR, Ekins S. Learning from COVID-19: How drug hunters can prepare for the next pandemic. Drug Discov Today 2023; 28:103723. [PMID: 37482237 PMCID: PMC10994687 DOI: 10.1016/j.drudis.2023.103723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023]
Abstract
Over 3 years, the SARS-CoV-2 pandemic killed nearly 7 million people and infected more than 767 million globally. During this time, our very small company was able to contribute to antiviral drug discovery efforts through global collaborations with other researchers, which enabled the identification and repurposing of multiple molecules with activity against SARS-CoV-2 including pyronaridine tetraphosphate, tilorone, quinacrine, vandetanib, lumefantrine, cetylpyridinium chloride, raloxifene, carvedilol, olmutinib, dacomitinib, crizotinib, and bosutinib. We highlight some of the key findings from this experience of using different computational and experimental strategies, and detail some of the challenges and strategies for how we might better prepare for the next pandemic so that potential antiviral treatments are available for future outbreaks.
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Affiliation(s)
- Ana C Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA.
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA.
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2
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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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3
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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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Chalcones from Angelica keiskei (ashitaba) inhibit key Zika virus replication proteins. Bioorg Chem 2022; 120:105649. [PMID: 35124513 PMCID: PMC9187613 DOI: 10.1016/j.bioorg.2022.105649] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/25/2022]
Abstract
Zika virus (ZIKV) is a dangerous human pathogen and no antiviral drugs have been approved to date. The chalcones are a group of small molecules that are found in a number of different plants, including Angelica keiskei Koidzumi, also known as ashitaba. To examine chalcone anti-ZIKV activity, three chalcones, 4-hydroxyderricin (4HD), xanthoangelol (XA), and xanthoangelol-E (XA-E), were purified from a methanol-ethyl acetate extract from A. keiskei. Molecular and ensemble docking predicted that these chalcones would establish multiple interactions with residues in the catalytic and allosteric sites of ZIKV NS2B-NS3 protease, and in the allosteric site of the NS5 RNA-dependent RNA-polymerase (RdRp). Machine learning models also predicted 4HD, XA and XA-E as potential anti-ZIKV inhibitors. Enzymatic and kinetic assays confirmed chalcone inhibition of the ZIKV NS2B-NS3 protease allosteric site with IC50s from 18 to 50 µM. Activity assays also revealed that XA, but not 4HD or XA-E, inhibited the allosteric site of the RdRp, with an IC50 of 6.9 µM. Finally, we tested these chalcones for their anti-viral activity in vitro with Vero cells. 4HD and XA-E displayed anti-ZIKV activity with EC50 values of 6.6 and 22.0 µM, respectively, while XA displayed relatively weak anti-ZIKV activity with whole cells. With their simple structures and relative ease of modification, the chalcones represent attractive candidates for hit-to-lead optimization in the search of new anti-ZIKV therapeutics.
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Cataneo AHD, Ávila EP, Mendes LADO, de Oliveira VG, Ferraz CR, de Almeida MV, Frabasile S, Duarte Dos Santos CN, Verri WA, Bordignon J, Wowk PF. Flavonoids as Molecules With Anti- Zika virus Activity. Front Microbiol 2021; 12:710359. [PMID: 34566915 PMCID: PMC8462986 DOI: 10.3389/fmicb.2021.710359] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/03/2021] [Indexed: 11/13/2022] Open
Abstract
Zika virus (ZIKV) is an arthropod-born virus that is mainly transmitted to humans by mosquitoes of the genus Aedes spp. Since its first isolation in 1947, only a few human cases had been described until large outbreaks occurred on Yap Island (2007), French Polynesia (2013), and Brazil (2015). Most ZIKV-infected individuals are asymptomatic or present with a self-limiting disease and nonspecific symptoms such as fever, myalgia, and headache. However, in French Polynesia and Brazil, ZIKV outbreaks led to the diagnosis of congenital malformations and microcephaly in newborns and Guillain-Barré syndrome (GBS) in adults. These new clinical presentations raised concern from public health authorities and highlighted the need for anti-Zika treatments and vaccines to control the neurological damage caused by the virus. Despite many efforts in the search for an effective treatment, neither vaccines nor antiviral drugs have become available to control ZIKV infection and/or replication. Flavonoids, a class of natural compounds that are well-known for possessing several biological properties, have shown activity against different viruses. Additionally, the use of flavonoids in some countries as food supplements indicates that these molecules are nontoxic to humans. Thus, here, we summarize knowledge on the use of flavonoids as a source of anti-ZIKV molecules and discuss the gaps and challenges in this area before these compounds can be considered for further preclinical and clinical trials.
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Affiliation(s)
| | - Eloah Pereira Ávila
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | | | | | - Camila Rodrigues Ferraz
- Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Sandra Frabasile
- Sección Virologia, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | | | - Waldiceu Aparecido Verri
- Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Juliano Bordignon
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Brazil
| | - Pryscilla Fanini Wowk
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Brazil
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7
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Lima CS, Mottin M, de Assis LR, Mesquita NCDMR, Sousa BKDP, Coimbra LD, Santos KBD, Zorn KM, Guido RVC, Ekins S, Marques RE, Proença-Modena JL, Oliva G, Andrade CH, Regasini LO. Flavonoids from Pterogyne nitens as Zika virus NS2B-NS3 protease inhibitors. Bioorg Chem 2021; 109:104719. [PMID: 33636437 PMCID: PMC8227833 DOI: 10.1016/j.bioorg.2021.104719] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/18/2022]
Abstract
Although the widespread epidemic of Zika virus (ZIKV) and its neurological complications are well-known there are still no approved drugs available to treat this arboviral disease or vaccine to prevent the infection. Flavonoids from Pterogyne nitens have already demonstrated anti-flavivirus activity, although their target is unknown. In this study, we virtually screened an in-house database of 150 natural and semi-synthetic compounds against ZIKV NS2B-NS3 protease (NS2B-NS3p) using docking-based virtual screening, as part of the OpenZika project. As a result, we prioritized three flavonoids from P. nitens, quercetin, rutin and pedalitin, for experimental evaluation. We also used machine learning models, built with Assay Central® software, for predicting the activity and toxicity of these flavonoids. Biophysical and enzymatic assays generally agreed with the in silico predictions, confirming that the flavonoids inhibited ZIKV protease. The most promising hit, pedalitin, inhibited ZIKV NS2B-NS3p with an IC50 of 5 μM. In cell-based assays, pedalitin displayed significant activity at 250 and 500 µM, with slight toxicity in Vero cells. The results presented here demonstrate the potential of pedalitin as a candidate for hit-to-lead (H2L) optimization studies towards the discovery of antiviral drug candidates to treat ZIKV infections.
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Affiliation(s)
- Caroline Sprengel Lima
- Laboratory of Antibiotics and Chemotherapeutics (LAQ), Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São José do Rio Preto, SP, Brazil
| | - Melina Mottin
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Leticia Ribeiro de Assis
- Laboratory of Antibiotics and Chemotherapeutics (LAQ), Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São José do Rio Preto, SP, Brazil
| | | | - Bruna Katiele de Paula Sousa
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Lais Durco Coimbra
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Karina Bispo-Dos- Santos
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States
| | - Rafael V C Guido
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - José Luiz Proença-Modena
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil.
| | - Luis Octavio Regasini
- Laboratory of Antibiotics and Chemotherapeutics (LAQ), Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São José do Rio Preto, SP, Brazil.
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8
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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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9
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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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10
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Poveda-Cuevas SA, Etchebest C, Barroso da Silva FL. Identification of Electrostatic Epitopes in Flavivirus by Computer Simulations: The PROCEEDpKa Method. J Chem Inf Model 2019; 60:944-963. [DOI: 10.1021/acs.jcim.9b00895] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sergio A. Poveda-Cuevas
- Universidade de São Paulo, Programa Interunidades em Bioinformática, Rua do Matão, 1010, BR, 05508-090 São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. Café, s/no−Campus da USP, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
- University of São Paulo-Université Sorbonne Paris Cité International Laboratory in Structural Bioinformatics, Av. do Café, s/no−FCFRP, Bloco B, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Catherine Etchebest
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015 Paris, France
- Equipe 2, Dynamique des Structures et des Interactions Moléculaires, Université Paris Diderot−Paris 7, INTS, 6 Rue Alexandre Cabanel, 75015 Paris, France
- Laboratoire d’Excellence GR-Ex, Paris, France
- University of São Paulo-Université Sorbonne Paris Cité International Laboratory in Structural Bioinformatics, Av. do Café, s/no−FCFRP, Bloco B, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Fernando L. Barroso da Silva
- Universidade de São Paulo, Programa Interunidades em Bioinformática, Rua do Matão, 1010, BR, 05508-090 São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. Café, s/no−Campus da USP, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
- University of São Paulo-Université Sorbonne Paris Cité International Laboratory in Structural Bioinformatics, Av. do Café, s/no−FCFRP, Bloco B, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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11
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Silva S, Shimizu JF, Oliveira DMD, Assis LRD, Bittar C, Mottin M, Sousa BKDP, Mesquita NCDMR, Regasini LO, Rahal P, Oliva G, Perryman AL, Ekins S, Andrade CH, Goulart LR, Sabino-Silva R, Merits A, Harris M, Jardim ACG. A diarylamine derived from anthranilic acid inhibits ZIKV replication. Sci Rep 2019; 9:17703. [PMID: 31776405 PMCID: PMC6881388 DOI: 10.1038/s41598-019-54169-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-transmitted Flavivirus, originally identified in Uganda in 1947 and recently associated with a large outbreak in South America. Despite extensive efforts there are currently no approved antiviral compounds for treatment of ZIKV infection. Here we describe the antiviral activity of diarylamines derived from anthranilic acid (FAMs) against ZIKV. A synthetic FAM (E3) demonstrated anti-ZIKV potential by reducing viral replication up to 86%. We analyzed the possible mechanisms of action of FAM E3 by evaluating the intercalation of this compound into the viral dsRNA and its interaction with the RNA polymerase of bacteriophage SP6. However, FAM E3 did not act by these mechanisms. In silico results predicted that FAM E3 might bind to the ZIKV NS3 helicase suggesting that this protein could be one possible target of this compound. To test this, the thermal stability and the ATPase activity of the ZIKV NS3 helicase domain (NS3Hel) were investigated in vitro and we demonstrated that FAM E3 could indeed bind to and stabilize NS3Hel.
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Affiliation(s)
- Suely Silva
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Jacqueline Farinha Shimizu
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Débora Moraes de Oliveira
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil
| | - Leticia Ribeiro de Assis
- Laboratory of Antibiotics and Chemotherapeutics, São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Cintia Bittar
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Melina Mottin
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goias, Goiânia, GO, 74605- 170, Brazil
| | - Bruna Katiele de Paula Sousa
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goias, Goiânia, GO, 74605- 170, Brazil
| | | | - Luis Octávio Regasini
- Laboratory of Antibiotics and Chemotherapeutics, São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Paula Rahal
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Alexander Luke 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
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, United States
| | - Carolina Horta Andrade
- LabMol - Laboratory of Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goias, Goiânia, GO, 74605- 170, Brazil
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology, Federal University of Uberlandia, Uberlândia, MG, Brasil
| | - Robinson Sabino-Silva
- Integrative Physiology and Salivary Nanobiotechnology Group, Federal University of Uberlandia, Uberlândia, MG, Brasil
| | - Andres Merits
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlandia, Uberlândia, MG, Brazil.
- São Paulo State University, IBILCE, S. José do Rio Preto, SP, Brazil.
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12
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Gonçalves RL, de Lima Menezes G, Sussuchi L, Moreli ML, Mottin M, Andrade CH, Pereira M, da Silva RA. Dynamic behavior of Dengue and Zika viruses NS1 protein reveals monomer–monomer interaction mechanisms and insights to rational drug design. J Biomol Struct Dyn 2019; 38:4353-4363. [DOI: 10.1080/07391102.2019.1677504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | - Luciane Sussuchi
- Núcleo Colaborativo de BioSistemas, Universidade Federal de Goiás, Jataí, GO, Brazil
| | - Marcos Lázaro Moreli
- Núcleo Colaborativo de BioSistemas, Universidade Federal de Goiás, Jataí, GO, Brazil
| | - Melina Mottin
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Universidade Federal de Goiás, Goiânia, GO, Brazil
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13
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Chesnut M, Muñoz LS, Harris G, Freeman D, Gama L, Pardo CA, Pamies D. In vitro and in silico Models to Study Mosquito-Borne Flavivirus Neuropathogenesis, Prevention, and Treatment. Front Cell Infect Microbiol 2019; 9:223. [PMID: 31338335 PMCID: PMC6629778 DOI: 10.3389/fcimb.2019.00223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/11/2019] [Indexed: 01/07/2023] Open
Abstract
Mosquito-borne flaviviruses can cause disease in the nervous system, resulting in a significant burden of morbidity and mortality. Disease models are necessary to understand neuropathogenesis and identify potential therapeutics and vaccines. Non-human primates have been used extensively but present major challenges. Advances have also been made toward the development of humanized mouse models, but these models still do not fully represent human pathophysiology. Recent developments in stem cell technology and cell culture techniques have allowed the development of more physiologically relevant human cell-based models. In silico modeling has also allowed researchers to identify and predict transmission patterns and discover potential vaccine and therapeutic candidates. This review summarizes the research on in vitro and in silico models used to study three mosquito-borne flaviviruses that cause neurological disease in humans: West Nile, Dengue, and Zika. We also propose a roadmap for 21st century research on mosquito-borne flavivirus neuropathogenesis, prevention, and treatment.
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Affiliation(s)
- Megan Chesnut
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura S. Muñoz
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Georgina Harris
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Dana Freeman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Lucio Gama
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Carlos A. Pardo
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Pamies
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Department of Physiology, University of Lausanne, Lausanne, Switzerland
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14
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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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15
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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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16
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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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17
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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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18
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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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19
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Devillers J. Repurposing drugs for use against Zika virus infection. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:103-115. [PMID: 29299939 DOI: 10.1080/1062936x.2017.1411642] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/25/2017] [Indexed: 06/07/2023]
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus for which there are no vaccines or specific therapeutics. To find drugs active on the virus is a complex, expensive and time-consuming process. The prospect of drug repurposing, which consists of finding new indications for existing drugs, is an interesting alternative to expedite drug development for specific diseases. In theory, drug repurposing is also able to respond much more rapidly to a crisis than a classical drug discovery process. Consequently, the methodology is attractive for vector-borne diseases that can emerge or re-emerge worldwide with the risk to become pandemic quickly. Different drugs, showing various structures, have been repurposed to be used against ZIKV infection. They are reviewed in this study and the conditions for their potential use in practice are discussed.
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20
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Mottin M, Braga RC, da Silva RA, Silva JHMD, Perryman AL, Ekins S, Andrade CH. Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity. Biochem Biophys Res Commun 2017; 492:643-651. [DOI: 10.1016/j.bbrc.2017.03.070] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/23/2017] [Accepted: 03/15/2017] [Indexed: 12/14/2022]
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21
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Nandy A, Basak SC. The Epidemic that Shook the World—The Zika Virus Rampage. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2017; 2:43-56. [DOI: 10.14218/erhm.2017.00018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Russo FB, Beltrão-Braga PCB. The impact of Zika virus in the brain. Biochem Biophys Res Commun 2017; 492:603-607. [PMID: 28108286 DOI: 10.1016/j.bbrc.2017.01.074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/16/2017] [Indexed: 11/27/2022]
Abstract
The recent outbreak of ZIKV in Brazil called the attention of the world because the effects of viral infection in the brain under development in fetuses. Consequences of vertical infection comprise brain malformation, especially microcephaly, eye and musculoskeletal abnormalities, among others. In adults, outcomes of infection include meningoencephalitis and Guillain-Barré Syndrome. Recent data specific suggest that neural progenitor cells are the main targets of ZIKV infection, causing massive cellular death and impairment in the neurogenesis process. Here we review the fetal and adult brain damage after ZIKV exposure, exploring models to study the mechanisms underlying the pathways related to microcephaly and cell death.
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Affiliation(s)
- Fabiele Baldino Russo
- University of São Paulo, Department of Surgery, Stem Cell Laboratory, São Paulo, São Paulo, 05508-270, Brazil
| | - Patricia Cristina Baleeiro Beltrão-Braga
- University of São Paulo, Department of Surgery, Stem Cell Laboratory, São Paulo, São Paulo, 05508-270, Brazil; School of Arts Sciences and Humanities, Department of Obstetrics, São Paulo, SP, 03828-000, Brazil.
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23
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Munjal A, Khandia R, Dhama K, Sachan S, Karthik K, Tiwari R, Malik YS, Kumar D, Singh RK, Iqbal HMN, Joshi SK. Advances in Developing Therapies to Combat Zika Virus: Current Knowledge and Future Perspectives. Front Microbiol 2017; 8:1469. [PMID: 28824594 PMCID: PMC5541032 DOI: 10.3389/fmicb.2017.01469] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/20/2017] [Indexed: 02/05/2023] Open
Abstract
Zika virus (ZIKV) remained largely quiescent for nearly six decades after its first appearance in 1947. ZIKV reappeared after 2007, resulting in a declaration of an international "public health emergency" in 2016 by the World Health Organization (WHO). Until this time, ZIKV was considered to induce only mild illness, but it has now been established as the cause of severe clinical manifestations, including fetal anomalies, neurological problems, and autoimmune disorders. Infection during pregnancy can cause congenital brain abnormalities, including microcephaly and neurological degeneration, and in other cases, Guillain-Barré syndrome, making infections with ZIKV a substantial public health concern. Genomic and molecular investigations are underway to investigate ZIKV pathology and its recent enhanced pathogenicity, as well as to design safe and potent vaccines, drugs, and therapeutics. This review describes progress in the design and development of various anti-ZIKV therapeutics, including drugs targeting virus entry into cells and the helicase protein, nucleosides, inhibitors of NS3 protein, small molecules, methyltransferase inhibitors, interferons, repurposed drugs, drugs designed with the aid of computers, neutralizing antibodies, convalescent serum, antibodies that limit antibody-dependent enhancement, and herbal medicines. Additionally, covalent inhibitors of viral protein expression and anti-Toll-like receptor molecules are discussed. To counter ZIKV-associated disease, we need to make rapid progress in developing novel therapies that work effectually to inhibit ZIKV.
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Affiliation(s)
- Ashok Munjal
- Department of Biochemistry and Genetics, Barkatullah UniversityBhopal, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah UniversityBhopal, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research InstituteBareilly, India
- *Correspondence: Kuldeep Dhama,
| | - Swati Sachan
- Immunology Section, ICAR-Indian Veterinary Research InstituteBareilly, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences UniversityChennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan SansthanMathura, India
| | - Yashpal S. Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research InstituteBareilly, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research InstituteBareilly, India
| | - Raj K. Singh
- ICAR-Indian Veterinary Research InstituteBareilly, India
| | - Hafiz M. N. Iqbal
- School of Engineering and Science, Tecnologico de Monterrey, Campus MonterreyMonterrey, Mexico
| | - Sunil K. Joshi
- Cellular Immunology Lab, Frank Reidy Research Center of Bioelectrics, Old Dominion University, NorfolkVA, United States
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