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Tropical Biomedicine ; : 129-137, 2023.
Article in English | WPRIM | ID: wpr-1006584


@#Chikungunya virus (CHIKV) is a neglected tropical pathogen that causes fever and long-lasting severe arthralgia. Despite its high morbidity, there is still no licensed specific therapeutic option for it. This study proposes a multi-epitope subunit vaccine candidate for CHIKV, designed using computational methods. It was based on the E2 spike glycoprotein in CHIKV, from which T- and B-cell epitopes were predicted and then refined. The pan HLA DR-binding epitope (PADRE) was added to this refined construct, then simulated compared with the native protein, where it was predicted to elicit more than twice the number of antibody titers. Thus, this construct is potentially effective against CHIKV, which further experimentation using live models would be able to verify. This study also demonstrates the feasibility of using rational tools in the future to further optimize vaccine design.

Rev. peru. med. exp. salud publica ; 38(4): 634-642, oct.-dic. 2021. tab, graf
Article in Spanish | LILACS | ID: biblio-1365939


RESUMEN El desarrollo y producción de vacunas seguras y eficaces contra la enfermedad por coronavirus 2019 (COVID-19) ofrece la esperanza para el control de la pandemia actual. Los eventos adversos posteriores a la inmunización son respuestas indeseadas o acontecimientos involuntarios que siguen a la vacunación, y que deben ser cuidadosamente vigilados, ya que todas las vacunas, incluyendo las desarrolladas contra el SARS-CoV-2, requieren cumplir con los criterios de seguridad para su administración en humanos. Se recopiló la información de la base de datos de PubMed/Medline durante los meses de agosto de 2020 a noviembre de 2021. La mayoría de los eventos adversos identificados en los ensayos clínicos fueron leves o moderados; sin embargo, se identificaron eventos trombóticos asociados a algunas vacunas basadas en vectores virales contra la COVID-19 en estudios de seguimiento, aunque se requiere la conclusión de los distintos estudios en curso y vigilancia poscomercialización para determinar todos los posibles eventos adversos y de especial interés.

ABSTRACT The development and production of safe and effective vaccines against coronavirus disease 2019 (COVID-19) provides hope for controlling the current pandemic. Adverse events following immunization are unwanted responses or unintended events that must be carefully monitored, as all vaccines, including those developed against SARS-CoV-2, are required to meet safety criteria for administration in humans. Information was collected from the PubMed/Medline database during the months of August 2020 to November 2021. Most adverse events reported in clinical trials were mild or moderate; however, thrombotic events associated with some viral vector-based vaccines against COVID-19 were identified in follow-up studies, although completion of the various ongoing studies and post-marketing surveillance is required to determine all potential adverse events, as well as those of special interest.

Humans , Male , Female , Efficacy , Clinical Trial, Phase III , SARS-CoV-2 , COVID-19 , Vaccines , Clinical Trial , Coronavirus , Drug-Related Side Effects and Adverse Reactions , Spike Glycoprotein, Coronavirus , Immunogenicity, Vaccine
Shanghai Journal of Preventive Medicine ; (12): 237-2021.
Article in Chinese | WPRIM | ID: wpr-882020


The severe acute syndrome coronavirus 2(SARS-CoV-2)is responsible for the global pandemic of 2019 novel coronavirus disease(COVID-19). Understanding the pathogenic mechanisms of SARS-CoV-2 is of great significance to the prevention and control of the COVID-19 epidemic. The spike(S)protein of SARS-CoV-2 is a major target of protective immunity. The mutations of S protein impact the transmission and pathogenic capacity of SARS-CoV-2. In addition, angiotensin-converting enzyme 2(ACE2)is the receptor of SARS-CoV-2 S protein and mediates viral entry into target cells. The genetic polymorphisms of the ACE2 gene may lead to the difference of incidence of COVID-19 among different populations. Protease can promote the infection of SARS-Cov-2 by activating the S protein. This review summarized the current understanding of the function and genetic variants of S protein, ACE2, and the related proteases. The synergistic effect of these three molecules on the susceptibility of SARS-CoV-2 infection was further discussed.

Chinese Herbal Medicines ; (4): 359-369, 2021.
Article in Chinese | WPRIM | ID: wpr-953645


Objective: To identify the safe and effective natural inhibitors of spike glycoprotein and main protease 3CLpro using potential natural antiviral compounds which are studied under various animal models and viral cell lines. Methods: First, compounds were retrieved from the PubChem database and predicted for their druggability using the MolSoft web server, and compounds having drug-like property were predicted for major adverse drug reactions like cardiotoxicity, hepatotoxicity, arrhythmia, myocardial infarction, and nephrotoxicity using ADVERpred. Docking of nontoxic antiviral compounds with spike glycoprotein and main protease 3CLpro was performed using AutoDock vina by PyRx 0.8 version. The stability of compound-protein interactions was checked by molecular dynamic (MD) simulation using Schrodinger Desmond software. Results: Based on the druggable and nontoxic profile, nine compounds were selected. Among them, Withanone from Withania somnifera showed the highest binding affinity and best fit at active sites 1 of spike glycoprotein (glycosylation site) and main protease 3CLpro via interacting with active site amino acid residues before and after MD simulation at 50 ns. Withanone, which may reduce the glycosylation of SARS-CoV-2 via interacting with Asn343 and inhibit viral replication. Conclusion: The current study reports Withanone as a non-toxic antiviral against SARS-CoV-2 and serve as a potential lead hit for further experimental validation.

Univ. salud ; 22(3,supl.1): 299-314, dic. 2020. tab, graf
Article in Spanish | LILACS, COLNAL | ID: biblio-1156997


Resumen Introducción: OVID-19 es una enfermedad respiratoria inédita que se reportó inicialmente como una neumonía atípica en diciembre de 2019. SARS-CoV-2, agente etiológico de esta patología, probablemente originado a partir de un virus de murciélago. La inesperada capacidad de transmisión y patogenicidad que adquirió este coronavirus transformó a COVID-19 en una pandemia de sintomatología variada y compleja. Objetivo: Analizar aspectos evolutivos, moleculares, biológicos, inmunológicos y epidemiológicos de esta enfermedad. Materiales y métodos: Se realizó una revisión narrativa de literatura científica publicada en Pubmed, sobre estos aspectos desde enero 2020. Resultados: SARS-CoV-2 es un nuevo coronavirus que utiliza su proteína superficial S para infectar células humanas que exhiben el receptor ACE2. Este patógeno se transmite por secreciones respiratorias e induce un incremento nocivo de mediadores químicos proinflamatorios en individuos vulnerables, reacción inmune conocida como tormenta de citoquinas. Esta respuesta hiper-inflamatoria es la causante de las lesiones alveolares que desencadenan la insuficiencia respiratoria observada en casos severos de COVID-19. Conclusiones: En individuos susceptibles, SARS-CoV-2 puede desencadenar una disfunción pulmonar que requiere soporte ventilatorio asistido y tratamiento con inmunosupresores. Se están desarrollando nuevas estrategias terapéuticas y de prevención para disminuir los elevados índices de contagio y la mortalidad asociados con COVID-19.

Abstract Introduction: COVID-19 is a new respiratory disease reported initially as an atypical pneumonia in December 2019. SARS-CoV-2, the etiological agent of this pathology, probably originated from a bat viral pathogen. The unexpected transmission and pathogenicity capacities that this coronavirus acquired turned COVID-19 into a pandemic with a wide and complex arrangement of symptoms. Objective: To analyze evolutionary, molecular, biological, immunological and epidemiological aspects of this disease. Materials and methods: A narrative review of the literature concerning these topics was conducted, which was published in Pubmed mostly from January 2020. Results: SARS-CoV-2 is a new coronavirus that uses its surface protein S to infect human cells that exhibit ACE2 receptors. This pathogen is transmitted through respiratory secretions and triggers a harmful increase in pro-inflammatory chemical mediators in vulnerable individuals, an immune reaction known as cytokine storm. This hyper-inflammatory response is the cause of the alveolar lesions behind the respiratory failure observed in severe cases of COVID-19. Conclusions: In susceptible individuals, SARS-CoV-2 triggers an acute respiratory distress syndrome that requires assisted ventilatory support and immunomodulatory therapy. New therapeutic and prevention strategies are being developed to reduce the high transmission and mortality rates associated with COVID-19.

Coronavirus Infections , Severe Acute Respiratory Syndrome , Spike Glycoprotein, Coronavirus , Betacoronavirus , Inflammation
NOVA publ. cient ; 18(spe35): 11-33, jul.-dic. 2020. tab, graf
Article in Spanish | LILACS | ID: biblio-1149463


Resumen El 31 de diciembre de 2019 la comisión municipal de salud de Wuhan (provincia de Hubei, China) informa sobre un inusitado brote de casos de neumonía en la ciudad. Posteriormente se determina que se trata de un nuevo coronavirus designado inicialmente como 2019-nCoV y posteriormente, SARS-CoV-2. El SARS-CoV-2 infecta y se replica en los neumocitos y macrófagos del sistema respiratorio específicamente en el parénquima pulmonar en donde reside el receptor celular ACE-2. Esta revisión describe aspectos relacionados con la transmisión, prevención, generalidades bioquímicas del SARS-CoV-2 y métodos diagnósticos del COVID-19. Inicialmente se describe la forma de transmisión del virus y algunas recomendaciones generales para su prevención. Posteriormente, se hace una descripción detallada de los aspectos bioquímicos del SARS-CoV-2, su ciclo infeccioso y la estructura de la proteína S, la cual está involucrada con el proceso de ingreso del virus a la célula. Finalmente, se describen los métodos y pruebas de laboratorio para el diagnóstico del COVID-19.

Abstract On December 31, 2019, Wuhan Municipal Health Commission (Hubei Province, China) reports on an unusual outbreak of pneumonia cases in the city. Subsequently it is determined that it is a new coronavirus initially designated as 2019-nCoV and later, SARS-CoV-2. SARS-CoV-2 infects and replicates in pneumocytes and macrophages of the respiratory system specifically in the lung parenchyma where the ACE-2 cell receptor resides. This review describes aspects related to the transmission, prevention, biochemical generalities of SARS-CoV-2 and diagnostic methods of COVID-19. Initially, it describes the form of virus transmission and general recommendations for its prevention. Subsequently, a detailed description is made of the biochemical aspects of SARS-CoV-2, its infectious cycle and the structure of protein S, which is involved in the process of entry of the virus into the cell. Finally, the methods and laboratory tests for the diagnosis of COVID-19 are described.

Humans , Coronavirus , Alveolar Epithelial Cells , Parenchymal Tissue , Macrophages
Journal of Peking University(Health Sciences) ; (6): 150-158, 2020.
Article in Chinese | WPRIM | ID: wpr-942155


OBJECTIVE@#To explore the natural mutations in Spike protein (S protein) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the changes of affinity between virus and associated receptors or drug molecules before and after the mutation based on whole length sequencing results.@*METHODS@#In the study, the bioinformatics analysis of all the published sequences of SARS-CoV-2 was conducted and thus the high frequency mutation sites were affirmed. Taking advantages of PolyPhen-2, the functional influence of each mutation in S protein was prospected. The 3D homologous modelling was performed by SWISS-MODEL to establish mutated S protein structural model, in which the protein-docking was then implemented with angiotensin-converting enzyme 2 (ACE2), dipeptidyl peptidase-4 (DPP4) and aminopeptidase N (APN) by ZDOCK, and the combining capacity of each mutated S protein evaluated by FiPD. Finally, the binding ability between mutated S proteins and anti-virus drugs were prospected and evaluated through AutoDock-Chimera 1.14.@*RESULTS@#The mutations in specific region of S protein had greater tendency to destroy the S protein function by analysis of mutated S protein structure. Protein-receptor docking analysis between naturally mutated S protein and host receptors showed that, in the case of spontaneous mutation, the binding ability of S protein to ACE2 tended to be weakened, while the binding ability of DPP4 tended to be enhanced, and there was no significant change in the binding ability of APN. According to the computational simulation results of affinity binding between small molecular drugs and S protein, the affinity of aplaviroc with S protein was significantly higher than that of other small molecule drug candidates.@*CONCLUSION@#The region from 400-1 100 amino acid in S protein of SARS-CoV-2 is the mutation sensitive part during natural state, which was more potential to mutate than other part in S protein during natural state. The mutated SARS-CoV-2 might tend to target human cells with DPP4 as a new receptor rather than keep ACE2 as its unique receptor for human infection. At the same time, aplaviroc, which was used for the treatment of human immunodeficiency virus (HIV) infection, may become a new promising treatment for SARS-CoV-2 and could be a potential choice for the development of SARS-CoV-2 drugs.

Humans , Antiviral Agents , COVID-19 , Peptidyl-Dipeptidase A/genetics , Point Mutation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics
Int. j. high dilution res ; 19(4): 2-9, 2020.
Article in English | LILACS, HomeoIndex | ID: biblio-1146533


IntroductionNosodes, the homeopathicpreparationssourcedfrom biological materials including clinical samples, cultures of organisms, and diseased tissues have been in use against the source-specific infections as well as other diseases. The nosodes have demonstrated some efficacy in managing epidemics, such as influenza, dengue, and leptospirosis.This article presents the need and process of development ofnosodes from the SARS-CoV-2 to explore its prophylactic and therapeutic potentials against certain related viral diseases.Materials and methodsA clinical sample of SARS-Cov-2 positive patient,based on the cycle threshold (CT) value of the qRT-PCR, heat-inactivated SARS-CoV-2, and spike glycoprotein all were processed for making nosodesas per the method described in Homoeopathy Pharmacopoeia of India.Molecular tests, such as qRT-PCR and sterility tests were performed to establish the live organisms, RNA material, and the absence of contamination.ResultsThree variants of CoronavirusNosodewere developed using a clinical sample,heat-inactivatedSARS-CoV-2, and spike glycoprotein.In potencies 3c and above, no detectableSARS-CoV-2 RNA material was found by PCR.The analytical results for nosodes were reported as compliant for sterility testing as per the IP.ConclusionThree variants of Coronavirus nosodes were preparedwhich need to be evaluated further through pre-clinical and clinical studies.(AU)

Humans , /pharmacology , Coronavirus Infections/therapy , Drug Compounding , Spike Glycoprotein, Coronavirus , Betacoronavirus , Virus Inactivation , Betacoronavirus/drug effects
Chinese Traditional and Herbal Drugs ; (24): 1804-1813, 2020.
Article in Chinese | WPRIM | ID: wpr-846485


Objective: To explore the main active components, key targets and signaling pathways of Qingfei Dayuan Granules in treating of COVID-19 based on network pharmacology and molecular docking. Methods: TCMSP, ETCM and YATCM databases were used to search the chemical constituents of Qingfei Dayuan Granules, and the threshold values of OB ≥ 30% and DL ≥0.18 were used to screen the potential active compounds. SIB and STITCH databases were used to query the targets corresponding to the active compounds, and the PPI network and network topology parameters were obtained by using STRING database. Cytoscape 3.6.0 was used to screen the hub targets. The key targets were analyzed by Gene Ontology (GO), the Kyoto Encyclopedia of genes and genomes (KEGG) pathway enrichment and tissue enrichment using DAVID 6.8 software. The molecular docking was performed by AutoDock Tools 1.5.6 software. Results: A total of 251 active compounds and 1 037 targets were obtained, 107 key targets and 185 corresponding compounds were screened. The key targets involved ESR1, AR, EGFR, KDR, MMP2, and 52 genes were coexpressed with ACE2. The results of GO function enrichment analysis showed that Qingfei Dayuan Granules mainly regulated the biological processes of cell surface signaling transduction, molecular function, phosphorylation and transcription. KEGG pathway enrichment mainly involved chemokine signaling pathway, T cell receptor signaling pathway, B cell receptor signaling pathway, natural killer cell mediated cytotoxicity and Toll like receptor signaling pathway. The results of tissue enrichment showed that the key gene expression sites were mainly in lung and epithelial cells, involving a variety of immune cells, such as T cells, B cells, lymphocytes, etc. Molecular docking showed that the compounds with good binding power to SARS-CoV-2-RBD-ACE2 complex in Qingfei Dayuan granules were mainly come from Bupleuri Radix, Codonopsis Radix, Anemarrhenae Rhizoma, and Glycyrrhizae Radix et Rhizoma. Saikosaponin, glycyrrhizic acid, anemarsaponin had good binding power with SARS-CoV-2-S-RBD-ACE2, which may be potential active components against SARS-CoV-2. Conclusion: Qingfei Dayuan Granules has the characteristics of multi-components, multi-targets and multi-pathway regulation. Saikosaponin, glycyrrhizic acid, and anemarsaponin may be the potential active components against SARS-CoV-2. The mechanisms of its treatment against COVID-19 may be related to the regulation of the co-expressed genes with ACE2, inhibition of inflammation and immune related signaling pathways, and the destruction of the complex structure of SARS-CoV-2-S-RBD-ACE2.

Virologica Sinica ; (6): 36-44, 2010.
Article in Chinese | WPRIM | ID: wpr-404192


A group of SARS-Iike coronaviruses(SL-CoV)have been identified in horseshoe bats.Despite SL-CoVs and SARS-CoV share identical genome structure and high-level sequence similarity,SL-CoV does not bind to the same cellular receptor as for SARS-CoV and the N-terminus of the S proteins only share 64% amino acid identity,suggesting there are fundamental differences between these two groups of coronaviruses.To gain insight into the basis of this difference,we established a recombinant adenovirus system expressing the S protein from SL-CoV(rAd-Rp3-S)to investigate its immune characterization.Our results showed that immunized mice generated strong humoral immune responses against the SL-CoV S protein.Moreover,a strong cellular immune response demonstrated by elevated IFN-γ and IL-6 levels was also observed in these mice.However,the induced antibody from these mice had weaker cross-reaction with the SARS-CoV S protein,and did not neutralize HIV pseudotyped with SARS-CoV S protein.These results demonstrated that the immunogenicity of the SL-CoV S protein is distinct from that of SARS-CoV,which may cause the immunological differences between human SARS-CoV and bat SL-CoV.Furthermore,the recombinant virus could serve as a potential vaccine candidate against bat SL-CoV infection.

Pesqui. vet. bras ; 28(3): 190-194, mar. 2008. ilus, tab
Article in English | LILACS | ID: lil-485053


Twelve Brazilian isolates and one reference vaccine strain of avian infectious bronchitis virus (IBV) were propagated in embryonating chicken eggs. The entire S1 glycoprotein gene of these viruses was analysed by reverse-transcriptase-polymerase chain reaction and restriction fragment length polymorphism (RT-PCR-RFLP), using the restriction enzymes HaeIII, XcmI and BstyI. The RFLP patterns led to the classification of these isolates into five distinct genotypes: A, B, C, D and Massachusetts. Five of twelve isolates were grouped in Massachusetts genotype and the remaining seven viruses were classified into four distinct genotypes: A (2), B (2), C (2) or D (1). Such genotyping classification agreed with previous immunological analysis for most of these viruses, highlighting the occurrence of a relevant variability among the IBV strains that are circulating in Brazilian commercial poultry flocks.

Doze isolados de campo do Brasil e uma estirpe de referência vacinal do vírus da bronquite infecciosa das aves (VBI) foram propagadas em ovos embrionados SPF. O gene S1 dessas amostras foi analisado por RT-PCR seguido de RFLP, empregando-se as enzimas de restrição HaeIII, XcmI e BstyI. Observou-se a existência de cinco genotipos diferentes: M (Massachusetts), A , B, C e D. Cinco dos doze isolados de campo do VBI foram classificados no genótipo Massachusetts e os sete vírus restantes foram classificados em quatro genotipos diferentes; A (2), B (2), C (2) ou D (1). Os resultados desta genotipagem concordam com os dados obtidos na análise imunológica previamente realizada para a maior parte destes vírus, destacando a ocorrência de uma variabilidade marcante entre os isolados do VBI que estão circulando nas granjas avícolas comerciais do Brasil.

Genotype , Reverse Transcriptase Polymerase Chain Reaction/methods , Vaccines/administration & dosage , Vaccines/adverse effects , Infectious bronchitis virus/isolation & purification