1
|
Saivish MV, Menezes GDL, da Silva RA, Fontoura MA, Shimizu JF, da Silva GCD, Teixeira IDS, Mistrão NFB, Hernandes VM, Rahal P, Sacchetto L, Pacca CC, Marques RE, Nogueira ML. Antiviral Activity of Quercetin Hydrate against Zika Virus. Int J Mol Sci 2023; 24:7504. [PMID: 37108665 PMCID: PMC10144977 DOI: 10.3390/ijms24087504] [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: 01/29/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 04/29/2023] Open
Abstract
Zika virus (ZIKV) has re-emerged in recent decades, leading to outbreaks of Zika fever in Africa, Asia, and Central and South America. Despite its drastic re-emergence and clinical impact, no vaccines or antiviral compounds are available to prevent or control ZIKV infection. This study evaluated the potential antiviral activity of quercetin hydrate against ZIKV infection and demonstrated that this substance inhibits virus particle production in A549 and Vero cells under different treatment conditions. In vitro antiviral activity was long-lasting (still observed 72 h post-infection), suggesting that quercetin hydrate affects multiple rounds of ZIKV replication. Molecular docking indicates that quercetin hydrate can efficiently interact with the specific allosteric binding site cavity of the NS2B-NS3 proteases and NS1-dimer. These results identify quercetin as a potential compound to combat ZIKV infection in vitro.
Collapse
Affiliation(s)
- Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Gabriela de Lima Menezes
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí 75801-615, GO, Brazil
| | | | - Marina Alves Fontoura
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Jacqueline Farinha Shimizu
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Gislaine Celestino Dutra da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Igor da Silva Teixeira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Natalia Franco Bueno Mistrão
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Victor Miranda Hernandes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Carolina Colombelli Pacca
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
- Departamento de Microbiologia, Faceres Medical School, São José do Rio Preto 15090-000, SP, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| |
Collapse
|
2
|
Poveda-Cuevas SA, Etchebest C, da Silva FLB. Self-association features of NS1 proteins from different flaviviruses. Virus Res 2022; 318:198838. [PMID: 35662566 DOI: 10.1016/j.virusres.2022.198838] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 12/22/2022]
Abstract
Flaviviruses comprise a large group of arboviral species that are distributed in several countries of the tropics, neotropics, and some temperate zones. Since they can produce neurological pathologies or vascular damage, there has been intense research seeking better diagnosis and treatments for their infections in the last decades. The flavivirus NS1 protein is a relevant clinical target because it is involved in viral replication, immune evasion, and virulence. Being a key factor in endothelial and tissue-specific modulation, NS1 has been largely studied to understand the molecular mechanisms exploited by the virus to reprogram host cells. A central part of the viral maturation processes is the NS1 oligomerization because many stages rely on these protein-protein assemblies. In the present study, the self-associations of NS1 proteins from Zika, Dengue, and West Nile viruses are examined through constant-pH coarse-grained biophysical simulations. Free energies of interactions were estimated for different oligomeric states and pH conditions. Our results show that these proteins can form both dimers and tetramers under conditions near physiological pH even without the presence of lipids. Moreover, pH plays an important role mainly controlling the regimes where van der Waals interactions govern their association. Finally, despite the similarity at the sequence level, we found that each flavivirus has a well-characteristic protein-protein interaction profile. These specific features can provide new hints for the development of binders both for better diagnostic tools and the formulation of new therapeutic drugs.
Collapse
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. do Café, s/no-Campus da USP, BR-14040-903 Ribeirão Preto, São Paulo, Brazil; University of São Paulo and Université de Paris International Laboratory in Structural Bioinformatics, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do Café, s/no-Campus da USP, Bloco B, BR-14040-903 Ribeirão Preto, São Paulo, Brazil.; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Catherine Etchebest
- Université Paris Cité, Biologie Intégrée du Globule Rouge, Equipe 2, INSERM, F-75015 Paris, France; University of São Paulo and Université de Paris International Laboratory in Structural Bioinformatics, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do Café, s/no-Campus da USP, 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. do Café, s/no-Campus da USP, BR-14040-903 Ribeirão Preto, São Paulo, Brazil; University of São Paulo and Université de Paris International Laboratory in Structural Bioinformatics, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do Café, s/no-Campus da USP, Bloco B, BR-14040-903 Ribeirão Preto, São Paulo, Brazil..
| |
Collapse
|
3
|
de Lima Menezes G, Vogel Saivish M, Lacerda Nogueira M, Alves da Silva R. Virtual screening of small natural compounds against NS1 protein of DENV, YFV and ZIKV. J Biomol Struct Dyn 2022; 41:2981-2991. [PMID: 35188085 DOI: 10.1080/07391102.2022.2042390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Diseases caused by viruses of the genus Flavivirus are among the main diseases that affect the world and they are a serious public health problem. Three of them stand out: Dengue, Yellow fever and Zika viruses. The non-structural protein 1 (NS1), encoded by this viral genus, in its dimeric form, plays important roles in the pathogenesis and RNA replication of these viruses. Therefore, the identification of chemicals with the potential to inhibit the formation of the NS1 protein dimer of DENV, YFV and ZIKV would enable them to act as a multi-target drug. For this, we selected conformations of the NS1 protein monomer with similar β-roll domain structure among the three virus species from conformations obtained from molecular dynamics simulations performed in GROMACS in 5 replicates of 150 ns for each species. After selecting the protein structures, a virtual screening of compounds from the natural products catalog of the ZINC database was performed using AutoDock Vina. The 100 best compounds were classified according efficiency criteria. Two compounds were observed in common to the species, with energy scores ranging from -9.2 kcal/mol to -10.1 kcal/mol. The results obtained here demonstrate the high similarity of NS1 proteins in the Flavivirus genus and high affinity for the same compounds; thus justifying the potential of these small molecules act in multitarget therapy.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | | |
Collapse
|
4
|
Peptides targeting dengue viral nonstructural protein 1 inhibit dengue virus production. Sci Rep 2020; 10:12933. [PMID: 32737386 PMCID: PMC7395749 DOI: 10.1038/s41598-020-69515-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Viruses manipulate the life cycle in host cells via the use of viral properties and host machineries. Development of antiviral peptides against dengue virus (DENV) infection has previously been concentrated on blocking the actions of viral structural proteins and enzymes in virus entry and viral RNA processing in host cells. In this study, we proposed DENV NS1, which is a multifunctional non-structural protein indispensable for virus production, as a new target for inhibition of DENV infection by specific peptides. We performed biopanning assays using a phage-displayed peptide library and identified 11 different sequences of 12-mer peptides binding to DENV NS1. In silico analyses of peptide-protein interactions revealed 4 peptides most likely to bind to DENV NS1 at specific positions and their association was analysed by surface plasmon resonance. Treatment of Huh7 cells with these 4 peptides conjugated with N-terminal fluorescent tag and C-terminal cell penetrating tag at varying time-of-addition post-DENV infection could inhibit the production of DENV-2 in a time- and dose-dependent manner. The inhibitory effects of the peptides were also observed in other virus serotypes (DENV-1 and DENV-4), but not in DENV-3. These findings indicate the potential application of peptides targeting DENV NS1 as antiviral agents against DENV infection.
Collapse
|
5
|
de Lima Menezes G, da Silva RA. Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1). J Biomol Struct Dyn 2020; 39:5657-5667. [PMID: 32657643 PMCID: PMC7443570 DOI: 10.1080/07391102.2020.1792992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Non-structural protein 1 (nsp1) is found in all Betacoronavirus genus, an important viral group that causes severe respiratory
human diseases. This protein has significant role in pathogenesis and it is considered a
probably major virulence factor. As it is absent in humans, it becomes an interesting
target of study, especially when it comes to the rational search for drugs, since it
increases the specificity of the target and reduces possible adverse effects that may be
caused to the patient. Using approaches in silico we seek to
study the behavior of nsp1 in solution to obtain its most stable conformation and find
possible drugs with affinity to all of them. For this purpose, complete model of nsp1 of
SARS-CoV-2 were predicted and its stability analyzed by molecular dynamics simulations in
five different replicas. After main pocket validation using two control drugs and the main
conformations of nsp1, molecular docking based on virtual screening were performed to
identify novel potential inhibitors from DrugBank database. It has been found 16 molecules
in common to all five nsp1 replica conformations. Three of them was ranked as the best
compounds among them and showed better energy score than control molecules that have
in vitro activity against nsp1 from SARS-CoV-2. The
results pointed out here suggest new potential drugs for therapy to aid the rational drug
search against COVID-19. Communicated by Ramaswamy H. Sarma
Collapse
|